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+---
+name: message_ids refactor plan
+overview: Overhaul MIRIX message management by removing the message_ids JSON array from Agent, eliminating redundant system message storage, and introducing in-memory message accumulation for agent steps. This resolves scaling bottlenecks, removes write contention, and eliminates wasteful write-then-delete churn.
+todos:
+  - id: in-memory-accumulator
+    content: Refactor Agent.step() and inner_step() to accumulate messages in-memory during the step loop instead of persisting after each inner_step
+    status: pending
+  - id: system-message-from-agent
+    content: Construct system message on the fly from agent_state.system instead of storing it as a Message row
+    status: pending
+  - id: orm-changes
+    content: Remove message_ids from Agent ORM and change messages relationship to lazy=noload
+    status: pending
+  - id: schema-changes
+    content: Update Pydantic schemas for Agent (remove message_ids)
+    status: pending
+  - id: agent-manager-rewrite
+    content: Rewrite AgentManager message methods to use query-based retrieval ordered by created_at, id
+    status: pending
+  - id: message-manager-updates
+    content: Add query-based fetch and bulk hard-delete methods for retention pruning; remove detached message cleanup
+    status: pending
+  - id: llm-api-layer
+    content: Update Anthropic and other LLM clients that assume messages[0] is the system message
+    status: pending
+  - id: retention-config
+    content: Add message_set_retention_count to Client ORM/schema; implement retention enforcement at end of step()
+    status: pending
+  - id: summarization-cleanup
+    content: Remove unneeded summarization code paths/settings for memory extraction flow and fail directly on context overflow
+    status: pending
+  - id: cleanup-managers
+    content: Replace message_ids manipulation in UserManager, ClientManager with bulk message hard-delete for retention pruning
+    status: pending
+  - id: api-client-sdk
+    content: Update REST API, server, SDK, and client layers to remove message_ids references
+    status: pending
+  - id: migration
+    content: Create SQL migration to add message_set_retention_count, indexes, remove legacy system messages, and drop message_ids
+    status: pending
+  - id: tests
+    content: "Update and add tests for new message management patterns: unit tests (mocked, no infra) for granular method behavior + integration tests invoking REST API endpoints to verify end-to-end correctness. Rewrite test_message_handling.py and test_agent_prompt_update.py in-place. Run via: ./scripts/run_tests_with_docker.sh --podman -s -v --log-cli-level=INFO"
+    status: pending
+  - id: chat-agent-deprecation
+    content: Make chat_agent fail loudly (NotImplementedError) when step() is invoked — it is broken by this refactor and will be fixed in a follow-up. Add deprecation notice to docs/ARCHITECTURE.md and a warning comment in agent.py at the chat_agent branch.
+    status: pending
+isProject: false
+---
+
+# Proposal: MIRIX Message Management Overhaul
+
+## 1. Problem
+
+MIRIX manages agent conversation history through a `message_ids` JSON column on the `agents` table. This is a flat array of message IDs representing the agent's "in-context memory." The design has several scaling and correctness problems:
+
+**Scaling bottleneck.** One meta-agent (and its sub-agents) exists per client, shared across all end-users. The `message_ids` array on a single agent row accumulates message IDs for every user. Every message operation (append, trim, clear) requires a read-modify-write of this array on the agent row, creating write contention when multiple workers process messages for different users concurrently.
+
+**Lost message state updates under concurrent load.** Because the `message_ids` array is read-modify-written as a whole, concurrent processing of messages for different users on the same agent causes lost updates. Worker A reads `message_ids`, Worker B reads the same `message_ids`, both append their respective message IDs, and whichever writes last silently overwrites the other's changes. This is a classic lost-update anomaly. Under production load — where a single agent processes messages for hundreds of millions of users simultaneously — this means message references are silently dropped, leading to missing conversation context, orphaned message rows, and non-deterministic agent behavior.
+
+**Eager loading hazard.** The `messages` relationship on the Agent ORM uses `lazy="selectin"`, which means loading an agent eagerly loads *all* of its messages into memory. For an agent serving millions of users, this is a ticking time bomb.
+
+**Redundant system message storage.** The system prompt is stored twice: once in `agent.system` (a column on the agent row) and once as a `Message` row at position 0 of `message_ids`. The code reads the system prompt from the message row, enriches it with memories, and sends it to the LLM. The `agent.system` column is the source of truth but the message row is what gets used at runtime.
+
+**Write-then-delete churn.** For the ECMS memory extraction path (the production use case), every agent step persists messages to the database, then immediately deletes them when `CLEAR_HISTORY_AFTER_MEMORY_UPDATE` fires. Sub-agents each store their own copies of the input messages, their LLM responses, tool results, and heartbeat messages -- all of which are deleted moments later. This is pure I/O overhead.
+
+## 2. Changes
+
+This proposal makes six interconnected changes:
+
+### 2.1 Store Message History In-Memory only
+
+Today, each call to `inner_step()` persists all new messages to the database via `append_to_in_context_messages`, then the next `inner_step()` reads them back via `get_in_context_messages` to build the LLM context. For memory extraction agents, these messages are written and then mostly deleted when `CLEAR_HISTORY_AFTER_MEMORY_UPDATE` fires.
+
+Each sub-agent (episodic, semantic, etc.) stores **its own redundant copy** of the input messages, LLM responses, tool results, heartbeat messages and message summaries in its `message_id` property.
+
+After a memory agent finishes, the history clearing logic resets the `message_ids` to only include: the system message & the current message-set that just processed. The heartbeats, tool calls, and any previously processed messages are cleared.
+
+**Change:**
+
+The `step()` loop will maintain an in-memory message list. Each `inner_step()` appends to this list instead of writing to the database. Messages are only persisted at the end of the `step()` loop, and only when the client's retention policy calls for it (see section 2.4)
+
+This eliminates:
+
+- All write-then-delete churn for the ECMS path
+- Redundant message copies across sub-agents (each sub-agent currently stores its own copy of the input)
+- The `save_agent()` call that writes `message_ids` after every step
+- The `delete_detached_messages_for_agent()` cleanup
+
+Observability is not affected: the `steps` table and LangFuse traces still capture all LLM interactions.
+
+For chaining (multiple steps in one `step()` call), the in-memory list grows across steps within the same invocation. The LLM sees the full conversation history without any database round-trips between steps.
+
+### 2.2 Store System Message Exclusively in Agent State
+
+Today, the system prompt is stored as a `Message` row with `role="system"` at position 0 of `message_ids`. The code in `inner_step()` reads it back, enriches it with retrieved memories, and mutates it in-memory before sending to the LLM. The `rebuild_system_prompt` method creates a new Message row and swaps `message_ids[0]` every time the prompt changes.
+
+**Change:**
+
+The system prompt will live exclusively in `agent_state.system`. When building the LLM message list, `inner_step()` constructs a system `Message` object on the fly from `agent_state.system`, enriches it with memories, and prepends it. No system message is stored in the messages table.
+
+This eliminates:
+
+- The duplicate storage of the system prompt
+- The `rebuild_system_prompt` dance of creating a new message row and swapping array positions
+- The convention that `messages[0]` is always the system message (a source of fragile assumptions across the codebase)
+- The `get_system_message()` method (callers read `agent_state.system` directly)
+
+### 2.3 Remove `message_ids` From Agent
+
+The `message_ids` JSON column on the `agents` table will be removed entirely. This is the main goal of this plan. For agent types that persist messages (retention > 0), conversation history is retrieved by querying the `messages` table directly, scoped by `(agent_id, user_id)` and ordered by `created_at`.
+
+**Ordering strategy:** Retrieval uses `ORDER BY created_at DESC, id DESC LIMIT N` to select the newest `N` retained sets, then reverses in-memory to chronological order (oldest -> newest) before prompt assembly.
+
+- `created_at` reflects processing order, which is what the LLM actually saw. Kafka already guarantees in-order delivery per user (messages are partitioned by `user_id`), so processing order matches real-world order.
+- `id` is the tiebreaker for deterministic ordering when timestamps match (a practically impossible edge-case).
+
+The `messages` relationship on the Agent ORM also changes from `lazy="selectin"` to `lazy="noload"` to prevent accidental eager loading.
+
+### 2.4 Configurable Message Retention Per Client
+
+Today, the history clearing behavior is hardcoded: after memory extraction, keep the system message + one "last edited memory item" summary + the most recent input message-set. Different clients have different needs:
+
+- A **batch client** (like ECMS) that sends an entire conversation thread as a single `save` call has no use for retained messages. It wants `N=0`.
+- An **interactive agent** that processes messages one at a time may benefit from seeing what it did in the last few invocations. It wants `N=5` or similar.
+
+**Change:** Add a `message_set_retention_count` field to the Client model. This integer controls how many recent **input message-sets** are retained in the database after processing.
+
+A **message-set** is defined as the input conversation payload from a single `step()` invocation. In the current ECMS path, this is typically persisted as one `messages` row whose `content` contains a packed multi-turn sequence (e.g., `[USER]... [ASSISTANT]...`). It does not include the agent's internal working messages (tool calls, tool results, heartbeats, intermediate assistant/tool chain messages). Those exist only in the in-memory accumulator during the step and are not persisted.
+
+- `message_set_retention_count = 0` -- No messages persisted. All agent work is in-memory only. (Default for memory extraction clients.)
+- `message_set_retention_count = N` -- Keep the N most recent input message-sets per `(agent_id, user_id)`. Older sets are hard-deleted.
+
+**Runtime contract for retention changes:** retrieval and pruning both enforce `N`.
+
+- **Read path:** when loading retained context at the start of `step()`, query only the newest `N` sets using `ORDER BY created_at DESC, id DESC LIMIT N`, then **always reverse in-memory** before prompt assembly so the LLM sees chronological order (oldest -> newest).
+- **Write path:** after persisting current input set(s), hard-delete rows older than the newest `N`.
+- This guarantees that changing `message_set_retention_count` at runtime takes effect on the **very next save/step** even before background cleanup completes.
+
+When retention >= 1, the start of a `step()` invocation loads the retained input message-sets from the DB into the in-memory accumulator, giving the agent context about what it processed recently. This DB load is capped with `LIMIT N` so only the newest retained sets are considered. Persistence at end-of-step writes only the current invocation's input message-set(s), then enforces retention by hard-deleting older sets.
+
+This replaces:
+
+- The `CLEAR_HISTORY_AFTER_MEMORY_UPDATE` environment variable (a global boolean)
+- The hardcoded "keep system message + last edited item" behavior
+- The per-agent-type branching logic that builds the "last edited memory item" summary
+
+**Note:** The MIRIX chat agent (`chat_agent` type) is a known casualty of this change. It requires retention of full step outputs (including assistant responses, tool calls, and tool results) for conversational continuity. This will be addressed in a follow-up.
+
+**Schema change:** Add `message_set_retention_count` (nullable Integer, default 0) to `[mirix/orm/client.py](mirix/orm/client.py)` and `[mirix/schemas/client.py](mirix/schemas/client.py)`.
+
+### 2.5 Remove In-Loop Summarization for Memory Extraction
+
+The in-loop summarization path is removed from this refactor scope. For the memory extraction path, if the prompt exceeds the context window, the step should fail with an explicit context-overflow error and skip memory extraction for that message. This keeps behavior simple, removes extra LLM calls, and aligns with the low expected frequency of oversized inputs.
+
+This is not only a behavior change: dead summarization branches used by this flow should be removed as part of the refactor (retry loops, summarizer-specific branching, and unused helper calls/settings in the memory extraction path).
+
+### 2.6 Keep "Last Edited Memory Item" but only as Ephemeral Chaining Context
+
+The current "last edited memory item" signal is useful context for follow-up reasoning, but it should no longer be persisted as a retained `messages` row.
+
+**Change:**
+
+- Preserve the behavior as an **in-memory-only** helper message when another chain step is about to run.
+- Do **not** write this synthetic summary to the `messages` table.
+- Do **not** include it in retained message-sets (`message_set_retention_count` controls persisted input sets only).
+
+This keeps the useful self-awareness signal for chaining while avoiding storage churn and retention pollution.
+
+Note: `occurred_at` is **not** added to the messages table. The real-world timestamp of a conversation is already stored where it matters — on the memory records themselves (episodic events, raw memories, etc.). Message ordering uses `created_at` (processing order), which is correct because Kafka guarantees in-order delivery per user and the LLM's context should reflect what it actually saw, not a reconstructed timeline.
+
+## 3. How It Works End-to-End
+
+### Batch Client (message_set_retention_count = 0)
+
+```
+1. Client save request → put_messages() → Kafka
+2. Worker consumes → _process_message_async() → server.send_messages()
+3. Agent step starts:
+   - N=0 → skip retained-set load (nothing to retrieve)
+   - Construct system message from `agent_state.system`
+4. LLM execution:
+   - Send [system_msg, new_input] to LLM
+   - Accumulate assistant/tool/intermediate messages in-memory only (not persisted)
+5. Memory tool fan-out (if triggered):
+   - EpisodicMemoryAgent.step():
+     - Constructs system message in-memory
+     - Sends [system_msg, input_copy] to LLM
+     - LLM returns episodic_memory_insert(...)
+     - Tool executes → writes to episodic_events table (this IS persisted)
+     - Accumulates messages in-memory (not persisted)
+   - SemanticMemoryAgent.step(): same pattern
+6. Retention write-back:
+   - `message_set_retention_count = 0` → do not persist input message-sets
+   - No retention prune needed
+7. No agent row updates (`message_ids` removed)
+8. Kafka offset handling unchanged in Phase 1 (existing auto-commit behavior remains)
+```
+
+### Real Time Client (message_set_retention_count = 3)
+
+```
+1. Client message/request enters `step()`
+2. Agent step starts:
+   - Load retained input sets with `ORDER BY created_at DESC, id DESC LIMIT N`
+   - Reverse in-memory to chronological order (oldest -> newest)
+   - Construct system message from `agent_state.system`
+3. LLM execution:
+   - Send [system_msg, retained_inputs..., new_input] to LLM
+   - Accumulate assistant/tool/intermediate messages in-memory only (not persisted)
+4. Memory tool fan-out (if triggered):
+   - Same sub-agent behavior as batch flow (memory table writes persist; message churn does not)
+5. Retention write-back:
+   - Persist current invocation input message-set(s) to `messages` (single row)
+6. Retention prune:
+   - Hard-delete rows older than newest `N` for `(agent_id, user_id)`
+7. No agent row updates (`message_ids` removed)
+8. Step completes with bounded retained context for next invocation
+```
+
+### MIRIX Chat Agent (known broken — follow-up)
+
+The chat agent requires retention of full step outputs (assistant responses, tool calls, tool results) for conversational continuity. This is not supported by the input-message-set-only retention model. The chat agent will be addressed in a follow-up change.
+
+### Context Overflow Behavior (no summarization)
+
+If the message-sequence exceeds the model context window, the step fails with a context-overflow error. No summarization retry is attempted. The worker records the failure and proceeds according to retry/DLQ policy in Phase 2.
+
+## 4. Edge Cases and Special Considerations
+
+**In-memory message loss on crash.** If a worker crashes mid-step, in-memory messages are lost. For memory agents this is acceptable because retained message-sets are ephemeral in this design. For chat agents, this is a behavior change: today a crash mid-step can leave partial messages in the DB. With this change, a crash can lose the entire step's in-memory message work. Note: this PR does **not** change Kafka offset commit semantics; existing auto-commit behavior remains. Manual commit/retry guarantees are deferred to Phase 2.
+
+**Context overflow now hard-fails extraction.** With summarization removed from scope, oversized inputs can fail memory extraction for that message. This is an accepted trade-off for Phase 1; Phase 2 retry/DLQ handling will surface these failures operationally.
+
+**Timestamp ties.** Two messages with the same `created_at` are disambiguated by `id`. In practice, messages within a step are created sequentially and differ by microseconds. The `id` tiebreaker gives a stable order for the rare tie case.
+
+**Chat agent is broken.** The MIRIX chat agent requires retention of full step outputs (assistant responses, tool calls, tool results) for conversational continuity. The input-message-set-only retention model does not support this. This is a known, accepted trade-off — the chat agent will be fixed in a follow-up.
+
+**Anthropic client assumption.** The Anthropic LLM client asserts `messages[0].role == "system"`. The caller (`inner_step`) will prepend the system message before passing to the LLM client, so this assertion continues to hold. The change is that the system message comes from `agent_state.system` rather than from a DB row.
+
+**"Last edited memory item" becomes ephemeral.** Today, the history clearing code builds a per-agent-type summary message (e.g., "Last edited memory item: [Episodic Event ID]: ...") and persists it as retained history. With configurable retention, retained history is input message-sets only. Keep this summary as optional **in-memory chaining context** only; do not persist it.
+
+## 5. Database Migration
+
+SQL migration steps (no Alembic dependency assumed):
+
+1. Add `message_set_retention_count` (nullable `Integer`, default `0`) to `clients`
+2. Add/adjust composite index on `(agent_id, user_id, is_deleted, created_at, id)` to `messages`
+3. Delete legacy system messages (`role = 'system'`)
+4. Drop `message_ids` from `agents`
+5. No eager backfill/prune is required for retention-size changes: read path `LIMIT N` guarantees immediate behavior after config change; write path pruning converges storage on subsequent saves
+
+### Migration rollout strategy (explicit)
+
+Important: updating ORM models does **not** alter existing tables by itself. `Base.metadata.create_all` only creates missing tables; it does not add/drop columns on existing tables. Use explicit SQL migration steps for column/index changes.
+
+Compatibility note:
+
+- Additive schema changes are backward-compatible for old code as long as new columns are nullable or have safe defaults.
+- For this plan, adding `clients.message_set_retention_count DEFAULT 0` is intentionally safe for existing clients and existing code.
+- Breaking changes are contract-phase changes (e.g., dropping `agents.message_ids`) and must happen only after code cutover.
+
+Recommended sequence:
+
+1. **Expand schema first**
+  - Add `clients.message_set_retention_count` (default `0`)
+  - Add/adjust read-path index for retention queries
+  - Keep `agents.message_ids` in place temporarily during this phase
+2. **Ship compatible code**
+  - New read path uses query-based retrieval (`DESC + LIMIT N`, then in-memory reverse)
+  - New write path uses retention hard-delete
+  - Do not depend on `agents.message_ids`
+3. **Data cleanup**
+  - Delete legacy system-message rows from `messages`
+  - (Optional) one-time cleanup SQL to remove obsolete/non-retained rows if desired
+4. **Contract schema**
+  - Drop `agents.message_ids` only after code no longer reads/writes it anywhere
+5. **Validation**
+  - Existing clients with no explicit setting behave as `N=0` (default), matching current memory-extraction expectations
+  - Changing `N` at runtime takes effect on first subsequent step because read path enforces `LIMIT N`
+
+## 6. How This Sets Up Phase 2 (Kafka Durability, Idempotency, Retries)
+
+This refactor is Phase 1. Kafka offset semantics are unchanged here (existing auto-commit remains enabled). Phase 2 will add manual Kafka offset commit, retry limits, and a dead-letter queue. The changes in this refactor are specifically designed to make Phase 2 straightforward.
+
+### 6.1 No Partial State Left Behind
+
+**Today's problem.** If a worker crashes mid-step, you get partial state: some messages are persisted in the messages table, some aren't; `message_ids` on the agent row may or may not have been updated; some memory inserts (episodic events, etc.) may have succeeded, others not. The Kafka offset is already auto-committed, so the message won't be retried.
+
+**After this refactor.** A crash mid-step leaves zero message state in the DB (for retention=0 clients). The only side effects are the actual memory writes (episodic events, semantic items, etc.). When Phase 2 switches to manual Kafka offset commit, a crash means the offset isn't committed, so the message gets redelivered. The retry sees a clean slate in the messages table — no partial message state to conflict with.
+
+### 6.2 No Agent Row Contention
+
+**Today's problem.** Every message operation does a read-modify-write on the agent row's `message_ids`. If two workers process messages for different users on the same agent concurrently, they race on the same row. With manual Kafka commit + retries, this gets worse — a retried message could interleave with a new message's processing.
+
+**After this refactor.** The agent row is never updated during message processing. Workers operating on different users are completely independent — they only touch the messages table, scoped by `(agent_id, user_id)`. Retries don't conflict with concurrent processing.
+
+### 6.3 Memory Writes Become the Idempotency Boundary
+
+With messages out of the picture, the only persistent side effects of processing a Kafka message are the actual memory writes:
+
+- `episodic_events` table inserts
+- `semantic_memory_items` table inserts
+- `resource_memory_items` table inserts
+- `procedural_memory_items` table inserts
+- `knowledge_vault_items` table inserts
+
+For Phase 2, these are the operations that need idempotency keys. A natural key would be the Kafka message offset + partition, or a hash of `(user_id, input_content)`. If a retry attempts to insert a memory that already exists (same idempotency key), it's a no-op.
+
+This refactor doesn't add idempotency keys yet, but it dramatically simplifies where they need to go. Instead of needing idempotency across messages table + agent row + memory tables, you only need it on the memory tables.
+
+## 7. Files to Modify
+
+### Agent Execution (`[mirix/agent/agent.py](mirix/agent/agent.py)`)
+
+The heaviest changes. Key modifications:
+
+- `inner_step()`: construct system message from `agent_state.system`; append new messages to an in-memory list instead of calling `append_to_in_context_messages`; load `in_context_messages` from the in-memory list (for chaining) or from DB query (for first step with retention > 0)
+- `step()`: maintain the in-memory message accumulator; at end of loop, check client's `message_set_retention_count` to decide whether/how much to persist; enforce retention limit by hard-deleting excess message-sets
+- `_handle_ai_response()`: remove the old persistence-oriented `should_clear_history` / `CLEAR_HISTORY_AFTER_MEMORY_UPDATE` block. Keep per-agent "last edited memory item" generation only as  in-memory chaining context (non-persistent).
+- `save_agent()`: remove `message_ids` write (this function may become a no-op or be removed)
+- Remove summarizer retry/in-place compression path for memory extraction flow; context-overflow should raise and fail the step.
+- Remove now-unused summarizer wiring in this flow (imports, settings checks, and helper branches that only supported summarize-and-retry behavior).
+
+### Agent Manager (`[mirix/services/agent_manager.py](mirix/services/agent_manager.py)`)
+
+Rewrite or remove message-related methods:
+
+- `get_in_context_messages()` -- query `messages` table by `(agent_id, user_id)`, no system message; apply `ORDER BY created_at DESC, id DESC LIMIT N` based on client `message_set_retention_count`
+- `get_system_message()` -- return `agent_state.system` directly, or remove
+- `append_to_in_context_messages()` -- just create message rows (no agent row update). Only called for persistence at end of step.
+- `prepend_to_in_context_messages()` -- remove (no summarizer prepend path needed after this refactor)
+- `set_in_context_messages()` -- remove entirely
+- `trim_older_in_context_messages()` -- hard-delete older messages via query
+- `trim_all_in_context_messages_except_system()` -- rename to `clear_user_messages()`, hard-delete via query
+- `reset_messages()` -- hard-delete user's messages directly
+- `rebuild_system_prompt()` -- just update `agent.system` column
+- `_generate_initial_message_sequence()` -- no longer creates a system message row
+- Remove `message_ids` from `_update_agent()` and Redis cache serialization
+
+### Message Manager (`[mirix/services/message_manager.py](mirix/services/message_manager.py)`)
+
+- Add `get_messages_for_agent_user(agent_id, user_id, limit=None)` -- query by `(agent_id, user_id)` with deterministic ordering; when used for retained-context load, call with `ORDER BY created_at DESC, id DESC LIMIT N`
+- Add `hard_delete_user_messages(agent_id, user_id)` -- bulk hard-delete for retention pruning
+- Remove `delete_detached_messages_for_agent()` and `cleanup_all_detached_messages()`
+
+### ORM Models
+
+- `[mirix/orm/message.py](mirix/orm/message.py)` -- Add/adjust composite index for retained-message-set queries on `(agent_id, user_id, is_deleted, created_at, id)`
+- `[mirix/orm/agent.py](mirix/orm/agent.py)` -- Remove `message_ids` column; change `messages` relationship to `lazy="noload"`
+- `[mirix/orm/client.py](mirix/orm/client.py)` -- Add `message_set_retention_count` column (nullable Integer, default 0)
+- `[mirix/orm/sqlalchemy_base.py](mirix/orm/sqlalchemy_base.py)` -- Remove `message_ids` from Redis cache serialization
+
+### Pydantic Schemas
+
+- `[mirix/schemas/agent.py](mirix/schemas/agent.py)` -- Remove `message_ids` from `AgentState` and `UpdateAgent`
+- `[mirix/schemas/client.py](mirix/schemas/client.py)` -- Add `message_set_retention_count` field
+
+### LLM API Layer
+
+- `[mirix/llm_api/anthropic_client.py](mirix/llm_api/anthropic_client.py)` -- Currently asserts `messages[0].role == "system"` and extracts it to a top-level param. Update to handle system message prepended by the caller.
+- `[mirix/llm_api/anthropic.py](mirix/llm_api/anthropic.py)` -- Same pattern.
+
+### Cleanup Managers
+
+- `[mirix/services/user_manager.py](mirix/services/user_manager.py)` -- Replace `agent.message_ids = [agent.message_ids[0]]` with bulk message hard-delete by `user_id` (retention path)
+- `[mirix/services/client_manager.py](mirix/services/client_manager.py)` -- Same, by `client_id`
+
+### API / Client / SDK
+
+- `[mirix/server/rest_api.py](mirix/server/rest_api.py)` -- Remove `message_ids` from `UpdateAgentRequest`
+- `[mirix/server/server.py](mirix/server/server.py)` -- Update if `save_agent` changes
+- `[mirix/client/client.py](mirix/client/client.py)`, `[mirix/client/remote_client.py](mirix/client/remote_client.py)`, `[mirix/local_client/local_client.py](mirix/local_client/local_client.py)`, `[mirix/sdk.py](mirix/sdk.py)` -- Remove `message_ids` references
+
+### Tests
+
+**Test strategy:** Two layers — unit tests (mocked, no infra) for granular method behavior, and integration tests invoking the REST API to verify end-to-end correctness.
+
+**Run tests via:**
+
+```bash
+./scripts/run_tests_with_docker.sh --podman -s -v --log-cli-level=INFO
+```
+
+**Format/lint before committing:**
+
+```bash
+poetry run black . && poetry run isort .
+```
+
+**Files to update (rewrite in-place):**
+
+- `[tests/test_message_handling.py](tests/test_message_handling.py)` — rewrite entirely: current tests cover `get_messages_by_ids` and `message_ids`-based `get_in_context_messages`, both of which are removed. Replace with unit tests for the new query-based retrieval methods (`get_messages_for_agent_user`, `hard_delete_user_messages`, retention pruning logic).
+- `[tests/test_agent_prompt_update.py](tests/test_agent_prompt_update.py)` — rewrite in-place: remove all `message_ids[0]` assertions (system message is no longer stored as a row). Replace with assertions that `agent_state.system` holds the updated prompt and that no system message row exists in the DB.
+
+**New unit tests to add:**
+
+- In-memory accumulator: messages accumulate across `inner_step()` calls without DB writes
+- Retention count = 0: no message rows written after `step()` completes
+- Retention count = N: exactly N input message-sets retained per `(agent_id, user_id)`; older sets hard-deleted
+- Context overflow: `step()` raises hard error, no summarization retry attempted
+- Ephemeral "last edited memory item": present in LLM prompt when chaining, absent from DB retention rows
+
+**New integration tests to add (REST API level):**
+
+- `PUT /agents/{id}` system prompt update: verify `agent_state.system` updated, no system message row created
+- `POST /messages` (save flow): verify retention=0 client writes no message rows; retention=N client writes and prunes correctly
+- Context overflow via API: verify error response, no partial state left in DB
+
+**Remove:**
+
+- All tests asserting summarizer retry/compression behavior in the memory extraction flow
+
+## 8. Chat Agent Deprecation
+
+The `chat_agent` agent type is **deprecated** as of this refactor. It requires retention of full step outputs (assistant responses, tool calls, tool results) for conversational continuity, which is incompatible with the input-message-set-only retention model introduced here.
+
+**Changes required in this refactor:**
+
+- In `mirix/agent/agent.py`: at the top of `step()`, check if `agent_state.agent_type == AgentType.chat_agent` and immediately raise `NotImplementedError` with a clear message pointing to the follow-up ticket.
+- In `mirix/server/server.py`: where `chat_agent` is handled (line 662), add a deprecation warning log before the `NotImplementedError` propagates.
+- In `docs/ARCHITECTURE.md`: add a **Deprecated** section or callout marking `chat_agent` as unsupported pending a follow-up redesign. Explain why (retention model incompatibility) and that it will be addressed in Phase 2.
+- In `mirix/schemas/agent.py`: add a comment on the `chat_agent` enum value marking it as deprecated.
+
+**Do not remove the `chat_agent` enum value** — it is needed for backward-compatible DB reads of existing agent rows.
+
+## 9. Instructions for Developers
+
+After merging this refactor, developers must reset their local databases before running the server or tests. This change removes legacy `agents.message_ids` behavior and introduces new retention semantics, so existing local DB state will be incompatible.
+
+Run `python scripts/reset_database.py` to reset your local database.
diff --git a/.cursorrules b/.cursorrules
index 01f87fc8c..270e434a0 100644
--- a/.cursorrules
+++ b/.cursorrules
@@ -74,7 +74,6 @@ The codebase is fully async-native. Violating these rules will break the server.
 #### 3. Agent Execution Flow
 - `step()` method is the main agent execution loop (like LangChain's AgentExecutor)
 - `inner_step()` handles single LLM interactions with tool calls
-- `save_agent()` persists agent state to database
 - Steps are logged to the `steps` table for audit/analytics (write-only)
 
 #### 4. Message Flow
@@ -117,9 +116,8 @@ Before suggesting changes, verify:
 2. **Do NOT** call `step_manager.get_step()` - steps are write-only audit logs
 3. **Do NOT** bypass `create_or_get_user()` - always ensure users exist first
 4. **Do NOT** create agents without proper `CreateAgent` schema objects
-5. **Do NOT** forget to persist agent state with `save_agent()`
-6. **Do NOT** use `message.step` relationship - it's never loaded in practice
-7. **Do NOT** add duplicate environment variables in settings.py
+5. **Do NOT** use `message.step` relationship - it's never loaded in practice
+6. **Do NOT** add duplicate environment variables in settings.py
 
 ### Testing Guidelines
 - Tests located in `tests/` directory
diff --git a/CLAUDE.md b/CLAUDE.md
index 5804fbfa0..9f15b14a8 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -40,6 +40,20 @@ python scripts/start_server.py --port 8531
 
 ## Running Tests
 
+The preferred way to run tests is via the dockerized test script, which handles infrastructure automatically:
+
+```bash
+# Full suite with verbose output (preferred)
+./scripts/run_tests_with_docker.sh --podman -s -v --log-cli-level=INFO
+
+# Pass any pytest args after the flags
+./scripts/run_tests_with_docker.sh --podman -s -v --log-cli-level=INFO -k test_message_handling
+./scripts/run_tests_with_docker.sh --podman -s -v --log-cli-level=INFO -m "not integration"
+```
+
+**Required env var for tests**: `GEMINI_API_KEY`
+
+### Running without Docker (manual infra)
 ```bash
 # Fast unit tests — no running server needed (~20s)
 pytest tests/test_memory_server.py -v
@@ -50,13 +64,8 @@ pytest -m "not integration" -v
 # Integration tests — requires server on port 8899
 python scripts/start_server.py --port 8899          # Terminal 1
 pytest tests/test_memory_integration.py -v -m integration -s   # Terminal 2
-
-# Full suite
-pytest -v
 ```
 
-**Required env var for tests**: `GEMINI_API_KEY`
-
 ## Common Dev Tasks
 
 ### Add a new API endpoint
@@ -74,6 +83,10 @@ pytest -v
 
 ### Format & lint
 ```bash
+# Preferred (poetry)
+poetry run black . && poetry run isort .
+
+# Alternatively via make
 make format   # ruff import sort + format
 make lint     # ruff check + pyright
 make check    # format + lint + test
diff --git a/docs/Mirix_async_native_changes.md b/docs/Mirix_async_native_changes.md
index 8fdb72e67..f6eef21f2 100644
--- a/docs/Mirix_async_native_changes.md
+++ b/docs/Mirix_async_native_changes.md
@@ -99,8 +99,8 @@ Bedrock) use their respective async SDK classes. Streaming responses are
 `asyncio.sleep()`.
 
 **Agent execution** (`mirix/agent/agent.py`)
-`step()`, `inner_step()`, `_get_ai_reply()`, `_handle_ai_response()`,
-`execute_tool_and_persist_state()`, and `save_agent()` are all async.
+`step()`, `inner_step()`, `_get_ai_reply()`, and `_handle_ai_response()`
+are all async.
 Built-in tools (core, memory, extras) are async. User-defined tools
 execute in `ToolExecutionSandbox` via `asyncio.create_subprocess_exec()`
 (no thread pool).
diff --git a/docs/architecture.html b/docs/architecture.html
index 338f20e1e..e411ccbee 100644
--- a/docs/architecture.html
+++ b/docs/architecture.html
@@ -1602,7 +1602,7 @@ <h3>In-Context Messages Per Agent</h3>
                         window sent to
                         the LLM on each call.
                         Messages are stored in the database and loaded via
-                        <code>agent_manager.get_in_context_messages()</code>.
+                        <code>message_manager.get_messages_for_agent_user()</code>.
                     </div>
                     <div class="code-block" style="margin-top: 15px;">
                         <pre><span class="comment"># Message structure for each agent</span>
@@ -1798,7 +1798,7 @@ <h3 style="color: #4ec9b0; margin: 30px 0 20px;">Step Execution Flow</h3>
                             <strong>inner_step()</strong>
                             <span style="color: #858585; margin-left: 10px;">Single async LLM call</span>
                             <div class="code-block" style="margin-top: 10px;">
-                                <pre>in_context_messages = <span class="keyword">await</span> self.agent_manager.<span class="function">get_in_context_messages</span>(...)
+                                <pre>in_context_messages = <span class="keyword">await</span> self.message_manager.<span class="function">get_messages_for_agent_user</span>(...)
 complete_prompt = <span class="keyword">await</span> self.<span class="function">build_system_prompt_with_memories</span>(raw_system)
 response = <span class="keyword">await</span> self.<span class="function">_get_ai_reply</span>(input_message_sequence)
 messages, continue_chaining, failed = <span class="keyword">await</span> self.<span class="function">_handle_ai_response</span>(response)</pre>
diff --git a/mirix/agent/__init__.py b/mirix/agent/__init__.py
index 44ad1a64b..d5d9619a2 100755
--- a/mirix/agent/__init__.py
+++ b/mirix/agent/__init__.py
@@ -23,7 +23,6 @@
     "app_utils",
     "Agent",
     "AgentState",
-    "save_agent",
     "BackgroundAgent",
     "CoreMemoryAgent",
     "EpisodicMemoryAgent",
@@ -35,7 +34,7 @@
     "SemanticMemoryAgent",
 ]
 
-from mirix.agent.agent import Agent, AgentState, save_agent
+from mirix.agent.agent import Agent, AgentState
 from mirix.agent.background_agent import BackgroundAgent
 from mirix.agent.core_memory_agent import CoreMemoryAgent
 from mirix.agent.episodic_memory_agent import EpisodicMemoryAgent
diff --git a/mirix/agent/agent.py b/mirix/agent/agent.py
index 0fbbeb141..47962dae6 100644
--- a/mirix/agent/agent.py
+++ b/mirix/agent/agent.py
@@ -7,14 +7,13 @@
 from datetime import datetime
 from typing import Callable, List, Optional, Tuple, Union
 
+import httpx
 import numpy as np
 import pytz
-import httpx
 
 from mirix.agent.tool_validators import validate_tool_args
 from mirix.constants import (
     CHAINING_FOR_MEMORY_UPDATE,
-    CLEAR_HISTORY_AFTER_MEMORY_UPDATE,
     CLI_WARNING_PREFIX,
     ERROR_MESSAGE_PREFIX,
     FIRST_MESSAGE_ATTEMPTS,
@@ -34,22 +33,21 @@
 from mirix.helpers import ToolRulesSolver
 from mirix.helpers.message_helpers import prepare_input_message_create
 from mirix.interface import AgentInterface
-from mirix.llm_api.helpers import calculate_summarizer_cutoff, get_token_counts_for_messages, is_context_overflow_error
+from mirix.llm_api.helpers import get_token_counts_for_messages, is_context_overflow_error
 from mirix.llm_api.llm_api_tools import create
 from mirix.llm_api.llm_client import LLMClient
 from mirix.log import get_logger
 from mirix.memory import summarize_messages
 from mirix.observability.context import get_trace_context, mark_observation_as_child
 from mirix.observability.langfuse_client import get_langfuse_client
-from mirix.schemas.agent import AgentState, AgentStepResponse, UpdateAgent
+from mirix.schemas.agent import AgentState, AgentStepResponse
 from mirix.schemas.block import BlockUpdate
 from mirix.schemas.client import Client
 from mirix.schemas.embedding_config import EmbeddingConfig
 from mirix.schemas.enums import MessageRole, ToolType
-from mirix.schemas.memory import ContextWindowOverview, Memory
+from mirix.schemas.memory import Memory
 from mirix.schemas.message import Message, MessageCreate
 from mirix.schemas.mirix_message_content import CloudFileContent, FileContent, ImageContent, TextContent
-from mirix.schemas.openai.chat_completion_request import Tool as ChatCompletionRequestTool
 from mirix.schemas.openai.chat_completion_response import ChatCompletionResponse
 from mirix.schemas.openai.chat_completion_response import Message as ChatCompletionMessage
 from mirix.schemas.openai.chat_completion_response import UsageStatistics
@@ -60,7 +58,7 @@
 from mirix.services.agent_manager import AgentManager
 from mirix.services.block_manager import BlockManager
 from mirix.services.episodic_memory_manager import EpisodicMemoryManager
-from mirix.services.helpers.agent_manager_helper import check_supports_structured_output, compile_memory_metadata_block
+from mirix.services.helpers.agent_manager_helper import check_supports_structured_output
 from mirix.services.knowledge_vault_manager import KnowledgeVaultManager
 from mirix.services.message_manager import MessageManager
 from mirix.services.procedural_memory_manager import ProceduralMemoryManager
@@ -68,26 +66,18 @@
 from mirix.services.semantic_memory_manager import SemanticMemoryManager
 from mirix.services.step_manager import StepManager
 from mirix.services.tool_execution_sandbox import ToolExecutionSandbox
-from mirix.settings import settings, summarizer_settings
-from mirix.system import (
-    get_contine_chaining,
-    get_token_limit_warning,
-    package_function_response,
-    package_summarize_message,
-    package_user_message,
-)
+from mirix.services.user_manager import UserManager
+from mirix.settings import settings
+from mirix.system import get_contine_chaining, get_token_limit_warning, package_function_response, package_user_message
 from mirix.tracing import trace_method
 from mirix.utils import (
     convert_timezone_to_utc,
-    count_tokens,
     get_friendly_error_msg,
     get_tool_call_id,
     get_utc_time,
     json_dumps,
     json_loads,
     log_telemetry,
-    num_tokens_from_functions,
-    num_tokens_from_messages,
     parse_json,
     printv,
     validate_function_response,
@@ -277,26 +267,6 @@ def __init__(
         # Logger that the Agent specifically can use, will also report the agent_state ID with the logs
         # Note: Logger is already initialized earlier in constructor
 
-    async def load_last_function_response(self):
-        """Load the last function response from message history."""
-        # Skip if actor not set yet (during __init__)
-        if self.actor is None:
-            return None
-
-        in_context_messages = await self.agent_manager.get_in_context_messages(
-            agent_state=self.agent_state, actor=self.actor, user=self.user
-        )
-        for i in range(len(in_context_messages) - 1, -1, -1):
-            msg = in_context_messages[i]
-            if msg.role == MessageRole.tool and msg.content[0].text:
-                try:
-                    response_json = json.loads(msg.content[0].text)
-                    if response_json.get("message"):
-                        return response_json["message"]
-                except (json.JSONDecodeError, KeyError):
-                    raise ValueError(f"Invalid JSON format in message: {msg.content[0].text}")
-        return None
-
     async def update_memory_if_changed(self, new_memory: Memory) -> bool:
         """
         Update internal memory object and system prompt if there have been modifications.
@@ -333,16 +303,12 @@ async def update_memory_if_changed(self, new_memory: Memory) -> bool:
                 auto_create_from_default=False,  # Don't auto-create here, only in step()
             )
             self.blocks_in_memory = Memory(
-                blocks=[
-                    await self.block_manager.get_block_by_id(block.id, user=self.user)
-                    for block in blocks_result
-                ]
+                blocks=[await self.block_manager.get_block_by_id(block.id, user=self.user) for block in blocks_result]
             )
 
             # NOTE: don't do this since re-buildin the memory is handled at the start of the step
             # rebuild memory - this records the last edited timestamp of the memory
             # TODO: pass in update timestamp from block edit time
-            # self.agent_state = self.agent_manager.rebuild_system_prompt(agent_id=self.agent_state.id, actor=self.user)
             return True
 
         return False
@@ -868,12 +834,6 @@ async def _get_ai_reply(
                 log_telemetry(self.logger, "_handle_ai_response finish generic Exception")
                 raise e
 
-            # check if we are going over the context window: this allows for articifial constraints
-            if response.usage.total_tokens > self.agent_state.llm_config.context_window:
-                # trigger summarization
-                log_telemetry(self.logger, "_get_ai_reply summarize_messages_inplace")
-                await self.summarize_messages_inplace(existing_file_uris=existing_file_uris)
-
             # return the response
             return response
 
@@ -1229,210 +1189,6 @@ async def _handle_ai_response(
 
             function_failed = overall_function_failed
 
-            # Handle context message clearing only if ALL functions succeeded
-            if not overall_function_failed:
-                should_clear_history = False
-
-                # Clear history for all non-chat agents when:
-                # 1. chaining=False (clear regardless of function calls), OR
-                # 2. finish_memory_update was called (clear when chaining completes)
-                if CLEAR_HISTORY_AFTER_MEMORY_UPDATE and not self.agent_state.is_type(AgentType.chat_agent):
-                    if not chaining:
-                        should_clear_history = True
-                        self.logger.info(f"should_clear_history=True (chaining=False)")
-                    else:
-                        for func_name in executed_function_names:
-                            if func_name == "finish_memory_update":
-                                should_clear_history = True
-                                self.logger.info(f"should_clear_history=True (finish_memory_update called)")
-                                break
-                else:
-                    self.logger.debug(
-                        f"Clearing skipped - CLEAR_HISTORY_AFTER_MEMORY_UPDATE={CLEAR_HISTORY_AFTER_MEMORY_UPDATE}, is_chat_agent={self.agent_state.is_type(AgentType.chat_agent)}"
-                    )
-
-                if should_clear_history:
-                    continue_chaining = False
-
-                    in_context_messages = await self.agent_manager.get_in_context_messages(
-                        agent_state=self.agent_state, actor=self.actor, user=self.user
-                    )
-                    self.logger.info(
-                        f"Clearing history - {len(in_context_messages)} messages -> keeping only system message"
-                    )
-                    message_ids = [message.id for message in in_context_messages]
-                    message_ids = [message_ids[0]]
-
-                    # show the last edited memory item
-                    memory_item = None
-                    memory_item_str = None
-
-                    if self.user is None:
-                        raise ValueError("User is required to clear history")
-
-                    if self.agent_state.name.endswith("episodic_memory_agent"):
-                        memory_item = await self.episodic_memory_manager.get_most_recently_updated_event(
-                            user=self.user,
-                            timezone_str=self.user.timezone,
-                        )
-                        if memory_item:
-                            memory_item = memory_item[0]
-                            memory_item_str = ""
-                            memory_item_str += "[Episodic Event ID]: " + memory_item.id + "\n"
-                            memory_item_str += (
-                                "[Event Occurred At]: " + memory_item.occurred_at.strftime("%Y-%m-%d %H:%M:%S") + "\n"
-                            )
-                            memory_item_str += "[Summary]: " + memory_item.summary + "\n"
-                            memory_item_str += "[Details]: " + memory_item.details + "\n"
-                            memory_item_str += (
-                                "[Last Modified]: "
-                                + memory_item.last_modify["operation"]
-                                + " at "
-                                + memory_item.last_modify["timestamp"].strftime("%Y-%m-%d %H:%M:%S")
-                                + "\n"
-                            )
-                            memory_item_str = memory_item_str.strip()
-
-                    elif self.agent_state.name.endswith("procedural_memory_agent"):
-                        memory_item = await self.procedural_memory_manager.get_most_recently_updated_item(
-                            user=self.user,
-                            timezone_str=self.user.timezone,
-                        )
-                        if memory_item:
-                            memory_item = memory_item[0]
-                            memory_item_str = ""
-                            memory_item_str += "[Procedural Memory ID]: " + memory_item.id + "\n"
-                            memory_item_str += "[Entry Type]: " + memory_item.entry_type + "\n"
-                            memory_item_str += "[Summary]: " + (memory_item.summary or "N/A") + "\n"
-                            memory_item_str += "[Steps]: " + "; ".join(memory_item.steps) + "\n"
-                            memory_item_str += (
-                                "[Last Modified]: "
-                                + memory_item.last_modify["operation"]
-                                + " at "
-                                + memory_item.last_modify["timestamp"].strftime("%Y-%m-%d %H:%M:%S")
-                                + "\n"
-                            )
-                            memory_item_str = memory_item_str.strip()
-
-                    elif self.agent_state.name.endswith("resource_memory_agent"):
-                        memory_item = await self.resource_memory_manager.get_most_recently_updated_item(
-                            user=self.user,
-                            timezone_str=self.user.timezone,
-                        )
-                        if memory_item:
-                            memory_item = memory_item[0]
-                            memory_item_str = ""
-                            memory_item_str += "[Resource Memory ID]: " + memory_item.id + "\n"
-                            memory_item_str += "[Title]: " + memory_item.title + "\n"
-                            memory_item_str += "[Summary]: " + (memory_item.summary or "N/A") + "\n"
-                            memory_item_str += "[Resource Type]: " + memory_item.resource_type + "\n"
-                            memory_item_str += "[Content]: " + memory_item.content + "\n"
-                            memory_item_str += (
-                                "[Last Modified]: "
-                                + memory_item.last_modify["operation"]
-                                + " at "
-                                + memory_item.last_modify["timestamp"].strftime("%Y-%m-%d %H:%M:%S")
-                                + "\n"
-                            )
-                            memory_item_str = memory_item_str.strip()
-
-                    elif self.agent_state.name.endswith("knowledge_vault_memory_agent"):
-                        memory_item = await self.knowledge_vault_manager.get_most_recently_updated_item(
-                            user=self.user,
-                            timezone_str=self.user.timezone,
-                        )
-
-                        # Check if finish_memory_update was one of the executed functions
-                        if "finish_memory_update" in executed_function_names and memory_item is None:
-                            memory_item_str = "No new knowledge vault items were added."
-
-                        if memory_item:
-                            memory_item = memory_item[0]
-                            memory_item_str = ""
-                            memory_item_str += "[Knowledge Vault ID]: " + memory_item.id + "\n"
-                            memory_item_str += "[Entry Type]: " + memory_item.entry_type + "\n"
-                            memory_item_str += "[Caption]: " + memory_item.caption + "\n"
-                            memory_item_str += "[Source]: " + memory_item.source + "\n"
-                            memory_item_str += "[Sensitivity]: " + memory_item.sensitivity + "\n"
-                            memory_item_str += "[Secret Value]: " + memory_item.secret_value + "\n"
-                            memory_item_str += (
-                                "[Last Modified]: "
-                                + memory_item.last_modify["operation"]
-                                + " at "
-                                + memory_item.last_modify["timestamp"].strftime("%Y-%m-%d %H:%M:%S")
-                                + "\n"
-                            )
-                            memory_item_str = memory_item_str.strip()
-
-                    elif self.agent_state.name.endswith("semantic_memory_agent"):
-                        memory_item = await self.semantic_memory_manager.get_most_recently_updated_item(
-                            user=self.user,
-                            timezone_str=self.user.timezone,
-                        )
-                        if memory_item:
-                            memory_item = memory_item[0]
-                            memory_item_str = ""
-                            memory_item_str += "[Semantic Memory ID]: " + memory_item.id + "\n"
-                            memory_item_str += "[Name]: " + memory_item.name + "\n"
-                            memory_item_str += "[Summary]: " + memory_item.summary + "\n"
-                            memory_item_str += "[Details]: " + (memory_item.details or "N/A") + "\n"
-                            memory_item_str += "[Source]: " + (memory_item.source or "N/A") + "\n"
-                            memory_item_str += (
-                                "[Last Modified]: "
-                                + memory_item.last_modify["operation"]
-                                + " at "
-                                + memory_item.last_modify["timestamp"].strftime("%Y-%m-%d %H:%M:%S")
-                                + "\n"
-                            )
-                            memory_item_str = memory_item_str.strip()
-
-                    elif self.agent_state.name.endswith("core_memory_agent"):
-                        memory_item_str = self.blocks_in_memory.compile() if self.blocks_in_memory else ""
-
-                    # Optionally create a summary message showing last edited memory item
-                    if memory_item_str:
-                        if self.agent_state.name.endswith("core_memory_agent"):
-                            message_content = "Current Full Core Memory:\n\n" + memory_item_str
-                        else:
-                            message_content = "Last edited memory item:\n\n" + memory_item_str
-
-                        # create a new message
-                        new_message = Message.dict_to_message(
-                            agent_id=self.agent_state.id,
-                            model=self.model,
-                            openai_message_dict={
-                                "role": "user",
-                                "content": message_content,
-                            },
-                        )
-
-                        # persist the message to the database
-                        persisted_message = await self.message_manager.create_message(
-                            new_message,
-                            actor=self.actor,  # Client for write operations (audit trail)
-                            client_id=self.client_id,  # From actor (Client)
-                            user_id=(
-                                self.user_id if self.user_id else UserManager.ADMIN_USER_ID
-                            ),  # Fallback to default user
-                        )
-
-                        # append the persisted message ID to the message list
-                        message_ids.append(persisted_message.id)
-
-                    # Clear history for all non-chat agents when should_clear_history is True
-                    # This applies to meta_memory_agent and all memory sub-agents
-                    await self.agent_manager.set_in_context_messages(
-                        agent_id=self.agent_state.id,
-                        message_ids=message_ids,
-                        actor=self.actor,
-                    )
-                    await self.message_manager.delete_detached_messages_for_agent(
-                        agent_id=self.agent_state.id, actor=self.actor
-                    )
-
-                    # Clear all messages since they were manually added to the conversation history
-                    messages = []
-
         else:
             # Standard non-function reply
             # Validate that we have content - LLM returned neither tool_calls nor content
@@ -1474,134 +1230,143 @@ async def step(
         input_messages: Union[Message, MessageCreate, List[Union[Message, MessageCreate]]],
         chaining: bool = True,
         max_chaining_steps: Optional[int] = None,
-        extra_messages: Optional[List[dict]] = None,
-        actor: Optional["Client"] = None,  # Client for write operations (audit trail)
-        user: Optional[User] = None,  # User for read operations (data scope)
+        actor: Optional["Client"] = None,  # Client
+        user: Optional[User] = None,
         **kwargs,
     ) -> MirixUsageStatistics:
-        """Run Agent.step in a loop, handling chaining via continue_chaining requests and function failures
+        """A "step" is one full invocation of an agent.
+
+        Run Agent.inner_step in a loop, handling chaining via continue_chaining requests and function failures
 
         Args:
             actor: Client object for write operations (updating messages, agent state) - audit trail
             user: User object for read operations (loading blocks, memory filtering) - data scope
         """
 
-        # Store actor for write operations
-        if actor:
-            self.actor = actor
+        from mirix.schemas.agent import AgentType
 
-        # Store user and load user's memory blocks
-        if user:
-            self.user = user
+        # chat_agent is deprecated - raise immediately
+        if self.agent_state.is_type(AgentType.chat_agent):
+            raise NotImplementedError(
+                "AgentType.chat_agent is deprecated and no longer supported. " "Use a memory agent type instead."
+            )
 
-            # Only load blocks for core_memory_agent (other agent types don't use blocks)
-            from mirix.schemas.agent import AgentType
+        if actor is None or user is None:
+            raise ValueError("Agent.step requires non-null actor and user.")
 
-            if self.agent_state.is_type(AgentType.core_memory_agent):
-                # Load existing blocks for this user, scoped by the client's write_scope.
-                # auto_create_from_default=True will create blocks from template if they don't exist for this scope.
-                # filter_tags_set_on_create is applied only when new blocks are created (e.g. from default template).
-                existing_blocks = await self.block_manager.get_blocks(
-                    user=self.user,
-                    any_scopes=self._block_scopes,
-                    filter_tags_set_on_create=self.block_filter_tags,
-                )
+        # Store actor/user context for this step invocation.
+        self.actor = actor
+        self.user = user
+
+        # Special case for Core Memory Agent: load blocks to use later in the step
+        if self.agent_state.is_type(AgentType.core_memory_agent):
+            # Load existing blocks for this user, scoped by the client's write_scope.
+            # auto_create_from_default=True will create blocks from template if they don't exist for this scope.
+            # filter_tags_set_on_create is applied only when new blocks are created (e.g. from default template).
+            existing_blocks = await self.block_manager.get_blocks(
+                user=self.user,
+                any_scopes=self._block_scopes,
+                filter_tags_set_on_create=self.block_filter_tags,
+            )
 
-                # Apply block_filter_tags to existing blocks (merge or replace).
-                # Skips blocks whose filter_tags already match the desired state
-                # (e.g. blocks just created from template with the same tags).
-                if self.block_filter_tags and existing_blocks:
-                    existing_blocks = await self._apply_block_filter_tags(existing_blocks)
+            # Apply block_filter_tags to existing blocks (merge or replace).
+            # Skips blocks whose filter_tags already match the desired state
+            # (e.g. blocks just created from template with the same tags).
+            if self.block_filter_tags and existing_blocks:
+                existing_blocks = await self._apply_block_filter_tags(existing_blocks)
 
-                # Load blocks into memory for core_memory_agent
-                self.blocks_in_memory = Memory(blocks=existing_blocks)
+            # Load blocks into memory for core_memory_agent
+            self.blocks_in_memory = Memory(blocks=existing_blocks)
 
-        # Load last function response from message history (deferred from __init__)
-        if self.actor is not None and self.last_function_response is None:
-            self.last_function_response = await self.load_last_function_response()
+        # Reset last function response for this step
+        self.last_function_response = None
 
         max_chaining_steps = max_chaining_steps or MAX_CHAINING_STEPS
 
-        first_input_message = input_messages[0] if isinstance(input_messages, list) else input_messages
-
-        # Convert MessageCreate objects to Message objects
-        if not isinstance(input_messages, list):
-            input_messages = [input_messages]
-        message_objects = [
-            (
-                m
-                if isinstance(m, Message)
-                else prepare_input_message_create(
-                    m,
-                    self.agent_state.id,
-                    wrap_user_message=False,
-                    wrap_system_message=True,
-                )
-            )
-            for m in input_messages
-        ]
-
-        extra_message_objects = (
-            [
-                prepare_input_message_create(
-                    m,
-                    self.agent_state.id,
-                    wrap_user_message=False,
-                    wrap_system_message=True,
+        # Normalize to runtime Message objects for downstream prompt assembly.
+        raw_input_messages = input_messages
+        if not isinstance(raw_input_messages, list):
+            raw_input_messages = [raw_input_messages]
+
+        # At the end of this normalization step we will end up with a list containing only one Message object
+        # (multiple messages are packed into a single Message object in the upstream caller)
+        # The step also converts it from a MessageCreate to a Message object
+        # to match compatability with the downstream prompt assembly.
+        normalized_input_messages: List[Message] = []
+        for m in raw_input_messages:
+            if isinstance(m, Message):
+                normalized_input_messages.append(m)
+            elif isinstance(m, MessageCreate):
+                normalized_input_messages.append(
+                    prepare_input_message_create(
+                        m,
+                        self.agent_state.id,
+                        wrap_user_message=False,
+                        wrap_system_message=True,
+                    )
                 )
-                for m in extra_messages
-            ]
-            if extra_messages is not None
-            else None
-        )
-        next_input_message = message_objects
-        counter = 0
-        total_usage = UsageStatistics()
-        step_count = 0
-
-        initial_message_count = len(
-            await self.agent_manager.get_in_context_messages(
-                agent_state=self.agent_state, actor=self.actor, user=self.user
-            )
-        )
-
-        if self.agent_state.is_type(AgentType.reflexion_agent):
-            # clear previous messages
-            in_context_messages = await self.agent_manager.get_in_context_messages(
-                agent_state=self.agent_state, actor=self.actor, user=self.user
-            )
-            in_context_messages = in_context_messages[:1]
-            await self.agent_manager.set_in_context_messages(
-                agent_id=self.agent_state.id,
-                message_ids=[message.id for message in in_context_messages],
+            else:
+                raise ValueError("input_messages items must be Message or MessageCreate, " f"got {type(m)}")
+
+        # Read retained history from the parent scope (for sub-agents) or from this
+        # agent's scope (for top-level agents/meta). This keeps sub-agent inputs as a
+        # single packed message while still providing parent retained context.
+        retention = (self.actor.message_set_retention_count or 0) if self.actor else 0
+        retention_agent_id = (
+            self.agent_state.parent_id or self.agent_state.id
+        )  # Retained messages in the DB are associated with the meta agent
+        should_read_retention = retention > 0 and self.actor and self.user_id
+        is_meta_agent = self.agent_state.is_type(AgentType.meta_memory_agent)
+        should_write_retention = retention > 0 and is_meta_agent and self.actor and self.user_id
+        retained_input_sets: List[Message] = []
+        if should_read_retention:
+            retained_input_sets = await self.message_manager.get_messages_for_agent_user(
+                agent_id=retention_agent_id,
+                user_id=self.user_id,
                 actor=self.actor,
+                limit=retention,
             )
 
+        # Chaining accumulator for the active agent loop only.
+        accumulated: List[Message] = list(retained_input_sets)
+        # Persist only the original input payload, never synthetic helper messages
+        # appended to iteration messages during meta-agent processing.
+        input_messages_for_persistence: List[Message] = list(normalized_input_messages)
+
         # Initialize the LLM client once per step to reuse across retries.
         llm_client = LLMClient.create(
             llm_config=self.agent_state.llm_config,
         )
 
+        if self.agent_state.is_type(AgentType.meta_memory_agent):
+            # Extract topics from retained context + current input messages.
+            try:
+                # make sure to include both retained context and current input messages in the search topic extraction
+                topics = await self._extract_topics_from_messages(retained_input_sets + normalized_input_messages)
+
+                if topics is not None:
+                    kwargs["topics"] = topics
+                else:
+                    printv(f"[Mirix.Agent.{self.agent_state.name}] WARNING: No topics extracted from input")
+
+            except Exception as e:
+                printv(f"[Mirix.Agent.{self.agent_state.name}] INFO: Error in extracting the topic from the input: {e}")
+                pass
+
+        # Main loop:ing
+        # Each iteration calls inner_step and then makes a decision about whether to continue chaining
+        # or to terminate the step. When chaining, the curren_input_messages are updated to reference
+        # a heartbeat message (e.g. "function failed", "continue chaining", etc.) and the previous input messages
+        # are added to the in-memory accumulator.
+        counter = 0
+        total_usage = UsageStatistics()
+        step_count = 0
+        loop_input_messages: List[Message] = list(normalized_input_messages)
         while True:
             kwargs["first_message"] = False
             kwargs["step_count"] = step_count
 
-            if self.agent_state.is_type(AgentType.meta_memory_agent, AgentType.chat_agent) and step_count == 0:
-                # When the agent first gets the screenshots, we need to extract the topic to search the query.
-                try:
-                    topics = await self._extract_topics_from_messages(next_input_message)
-
-                    if topics is not None:
-                        kwargs["topics"] = topics
-                    else:
-                        printv(f"[Mirix.Agent.{self.agent_state.name}] WARNING: No topics extracted from screenshots")
-
-                except Exception as e:
-                    printv(
-                        f"[Mirix.Agent.{self.agent_state.name}] INFO: Error in extracting the topic from the screenshots: {e}"
-                    )
-                    pass
-
+            loop_iteration_messages = list(loop_input_messages)
             if self.agent_state.is_type(AgentType.meta_memory_agent) and step_count == 0:
                 meta_message = prepare_input_message_create(
                     MessageCreate(
@@ -1613,32 +1378,29 @@ async def step(
                     wrap_user_message=False,
                     wrap_system_message=True,
                 )
-                next_input_message.append(meta_message)
+                loop_iteration_messages.append(meta_message)
 
             step_response = await self.inner_step(
-                first_input_messge=first_input_message,
-                messages=next_input_message,
-                extra_messages=extra_message_objects,
-                initial_message_count=initial_message_count,
+                messages=loop_iteration_messages,
+                accumulated=accumulated,
                 chaining=chaining,
                 llm_client=llm_client,
+                retained_count=len(retained_input_sets),
                 **kwargs,
             )
 
             continue_chaining = step_response.continue_chaining
             function_failed = step_response.function_failed
-            token_warning = step_response.in_context_memory_warning
             usage = step_response.usage
 
+            # Accumulate step messages for next chaining iteration
+            accumulated = accumulated + step_response.messages
+
             step_count += 1
             total_usage += usage
             counter += 1
             self.interface.step_complete()
 
-            # logger.debug("Saving agent state")
-            # save updated state
-            await save_agent(self)
-
             # Chain stops
             if not chaining and (not function_failed):
                 printv(f"[Mirix.Agent.{self.agent_state.name}] INFO: No chaining, stopping after one step")
@@ -1649,60 +1411,66 @@ async def step(
                     warning_content = "[System Message] You have reached the maximum chaining steps. Please call 'send_message' to send your response to the user."
                 else:
                     warning_content = "[System Message] You have reached the maximum chaining steps. Please call 'finish_memory_update' to end the chaining."
-                next_input_message = Message.dict_to_message(
-                    agent_id=self.agent_state.id,
-                    model=self.model,
-                    openai_message_dict={
-                        "role": "user",
-                        "content": warning_content,
-                    },
-                )
+                loop_input_messages = [
+                    Message.dict_to_message(
+                        agent_id=self.agent_state.id,
+                        model=self.model,
+                        openai_message_dict={
+                            "role": "user",
+                            "content": warning_content,
+                        },
+                    )
+                ]
                 continue  # give agent one more chance to respond
             elif max_chaining_steps is not None and counter > max_chaining_steps:
                 printv(
                     f"[Mirix.Agent.{self.agent_state.name}] INFO: Hit max chaining steps, stopping after {counter} steps"
                 )
                 break
-            # Chain handlers
-            elif token_warning and summarizer_settings.send_memory_warning_message:
-                assert self.agent_state.created_by_id is not None
-                next_input_message = Message.dict_to_message(
-                    agent_id=self.agent_state.id,
-                    model=self.model,
-                    openai_message_dict={
-                        "role": "user",  # TODO: change to system?
-                        "content": get_token_limit_warning(),
-                    },
-                )
-                continue  # always chain
             elif function_failed:
                 assert self.agent_state.created_by_id is not None
-                next_input_message = Message.dict_to_message(
-                    agent_id=self.agent_state.id,
-                    model=self.model,
-                    openai_message_dict={
-                        "role": "user",  # TODO: change to system?
-                        "content": get_contine_chaining(FUNC_FAILED_HEARTBEAT_MESSAGE),
-                    },
-                )
+                loop_input_messages = [
+                    Message.dict_to_message(
+                        agent_id=self.agent_state.id,
+                        model=self.model,
+                        openai_message_dict={
+                            "role": "user",  # TODO: change to system?
+                            "content": get_contine_chaining(FUNC_FAILED_HEARTBEAT_MESSAGE),
+                        },
+                    )
+                ]
                 continue  # always chain
             elif continue_chaining:
                 assert self.agent_state.created_by_id is not None
-                next_input_message = Message.dict_to_message(
-                    agent_id=self.agent_state.id,
-                    model=self.model,
-                    openai_message_dict={
-                        "role": "user",  # TODO: change to system?
-                        "content": get_contine_chaining(REQ_HEARTBEAT_MESSAGE),
-                    },
-                )
+                loop_input_messages = [
+                    Message.dict_to_message(
+                        agent_id=self.agent_state.id,
+                        model=self.model,
+                        openai_message_dict={
+                            "role": "user",  # TODO: change to system?
+                            "content": get_contine_chaining(REQ_HEARTBEAT_MESSAGE),
+                        },
+                    )
+                ]
                 continue  # always chain
             # Mirix no-op / yield
             else:
                 break
 
-        # Save the message_ids
-        await save_agent(self)
+        # Retention write-back: persist input messages and prune old ones if configured
+        if should_write_retention and input_messages_for_persistence:
+            await self.message_manager.create_many_messages(
+                input_messages_for_persistence,
+                actor=self.actor,
+                client_id=self.client_id,
+                user_id=self.user_id,
+            )
+            await self.message_manager.hard_delete_user_messages_for_agent(
+                agent_id=self.agent_state.id,
+                user_id=self.user_id,
+                actor=self.actor,
+                keep_newest_n=retention,
+            )
 
         return MirixUsageStatistics(**total_usage.model_dump(), step_count=step_count)
 
@@ -1740,7 +1508,9 @@ async def build_system_prompt_with_memories(
 
         # Prepare embedding for semantic search
         if key_words != "" and search_method == "embedding":
-            embedded_text = await (await embedding_model(self.agent_state.embedding_config)).get_text_embedding(key_words)
+            embedded_text = await (await embedding_model(self.agent_state.embedding_config)).get_text_embedding(
+                key_words
+            )
             embedded_text = np.array(embedded_text)
             embedded_text = np.pad(
                 embedded_text,
@@ -2210,47 +1980,92 @@ async def construct_system_message(self, message: str) -> str:
         """
         topics = await self._extract_topics_from_message(message)
 
-        in_context_messages = await self.agent_manager.get_in_context_messages(
-            agent_state=self.agent_state, actor=self.actor, user=self.user
-        )
-        raw_system = (
-            in_context_messages[0].content[0].text
-            if in_context_messages and in_context_messages[0].role == MessageRole.system
-            else ""
-        )
+        # Use system prompt directly from agent state (no longer stored as a DB message)
+        raw_system = self.agent_state.system or ""
 
         # Build the complete system prompt with memories
         complete_system_prompt, _ = await self.build_system_prompt_with_memories(raw_system=raw_system, topics=topics)
 
         return complete_system_prompt
 
+    async def summarize_and_replace_retained_messages(
+        self,
+        retained_messages: List[Message],
+        existing_file_uris: Optional[List[str]] = None,
+    ) -> Message:
+        """Summarize retained input-set messages and replace them in the DB.
+
+        Calls the LLM to produce a summary of the retained messages, persists
+        the summary as a single ``message_type='summary'`` row, then hard-deletes
+        the original retained rows.
+
+        Returns the new summary ``Message`` for use in the in-memory accumulator.
+        """
+        printv(
+            f"[Mirix.Agent.{self.agent_state.name}] INFO: "
+            f"Summarizing {len(retained_messages)} retained messages to recover from context overflow"
+        )
+
+        summary_text = await summarize_messages(
+            agent_state=self.agent_state,
+            message_sequence_to_summarize=retained_messages,
+            existing_file_uris=existing_file_uris,
+        )
+
+        retention_agent_id = self.agent_state.parent_id or self.agent_state.id
+        summary_msg = Message(
+            agent_id=retention_agent_id,
+            role=MessageRole.user,
+            content=[TextContent(text=summary_text)],
+            user_id=self.user_id,
+            message_type="summary",
+        )
+
+        await self.message_manager.create_message(
+            summary_msg,
+            actor=self.actor,
+            client_id=self.client_id,
+            user_id=self.user_id,
+        )
+
+        for msg in retained_messages:
+            await self.message_manager.delete_message_by_id(
+                message_id=msg.id,
+                actor=self.actor,
+            )
+
+        printv(
+            f"[Mirix.Agent.{self.agent_state.name}] INFO: "
+            f"Replaced {len(retained_messages)} retained messages with summary (id={summary_msg.id})"
+        )
+
+        return summary_msg
+
     async def inner_step(
         self,
-        first_input_messge: Message,
         messages: Union[Message, List[Message]],
-        first_message: bool = False,
-        first_message_retry_limit: int = FIRST_MESSAGE_ATTEMPTS,
-        skip_verify: bool = False,
+        accumulated: Optional[List[Message]] = None,
         stream: bool = False,  # TODO move to config?
         step_count: Optional[int] = None,
-        metadata: Optional[dict] = None,
-        summarize_attempt_count: int = 0,
         force_response: bool = False,
         topics: Optional[str] = None,
         retrieved_memories: Optional[dict] = None,
         display_intermediate_message: any = None,
         request_user_confirmation: Optional[Callable] = None,
         existing_file_uris: Optional[List[str]] = None,
-        extra_messages: Optional[List[dict]] = None,
-        initial_message_count: Optional[int] = None,
         return_memory_types_without_update: bool = False,
         message_queue: Optional[any] = None,
         chaining: bool = True,
         llm_client: Optional[LLMClient] = None,
+        retained_count: int = 0,
+        _summarization_attempted: bool = False,
         **kwargs,
     ) -> AgentStepResponse:
         """Runs a single step in the agent loop (generates at most one LLM call)"""
 
+        if accumulated is None:
+            accumulated = []
+
         try:
             # Log the start of each reasoning step
             printv(
@@ -2259,16 +2074,8 @@ async def inner_step(
             if topics:
                 printv(f"[Mirix.Agent.{self.agent_state.name}] INFO: Step topics: {topics}")
 
-            # previous_in_context_messages = self.agent_state.message_ids
-            # new_message_ids = self.agent_manager.get_agent_by_id(agent_id=self.agent_state.id, actor=self.user).message_ids
-
-            # Step 0: get in-context messages and get the raw system prompt
-            in_context_messages = await self.agent_manager.get_in_context_messages(
-                agent_state=self.agent_state, actor=self.actor, user=self.user
-            )
-
-            assert in_context_messages[0].role == MessageRole.system
-            raw_system = in_context_messages[0].content[0].text
+            # Step 0: build the system message on-the-fly from agent_state.system + memories
+            raw_system = self.agent_state.system or ""
 
             # Build the complete system prompt with memories
             complete_system_prompt, retrieved_memories = await self.build_system_prompt_with_memories(
@@ -2277,24 +2084,26 @@ async def inner_step(
                 retrieved_memories=retrieved_memories,
             )
 
-            in_context_messages[0].content[0].text = complete_system_prompt
+            system_msg = Message.dict_to_message(
+                agent_id=self.agent_state.id,
+                model=self.model,
+                openai_message_dict={"role": "system", "content": complete_system_prompt},
+            )
 
             # Step 1: add user message
             if isinstance(messages, Message):
                 messages = [messages]
 
             if not all(isinstance(m, Message) for m in messages):
-                raise ValueError(f"messages should be a Message or a list of Message, got {type(messages)}")
-
-            input_message_sequence = in_context_messages + messages
-
-            if extra_messages is not None:
-                input_message_sequence = (
-                    input_message_sequence[:initial_message_count]
-                    + extra_messages
-                    + input_message_sequence[initial_message_count:]
+                message_types = [type(m).__name__ for m in messages]
+                raise ValueError(
+                    "messages should be a Message or a list of Message, "
+                    f"got container={type(messages)}, elements={message_types}"
                 )
 
+            # Build sequence: [system] + accumulated (prior chaining steps) + current messages
+            input_message_sequence = [system_msg] + accumulated + messages
+
             if len(input_message_sequence) > 1 and input_message_sequence[-1].role != "user":
                 printv(
                     f"[Mirix.Agent.{self.agent_state.name}] WARNING: {CLI_WARNING_PREFIX}Attempting to run ChatCompletion without user as the last message in the queue"
@@ -2303,7 +2112,6 @@ async def inner_step(
             # Step 2: send the conversation and available functions to the LLM
             response = await self._get_ai_reply(
                 message_sequence=input_message_sequence,
-                first_message=first_message,
                 stream=stream,
                 step_count=step_count,
                 existing_file_uris=existing_file_uris,
@@ -2335,7 +2143,7 @@ async def inner_step(
             for response_choice in response.choices:
                 response_message = response_choice.message
                 tmp_response_messages, continue_chaining, function_failed = await self._handle_ai_response(
-                    first_input_messge,  # give the last message to the function so that other agents can see this message through funciton_calls
+                    messages[0],  # Input messages are always packed into a single MessageCreate object
                     response_message,
                     existing_file_uris=existing_file_uris,
                     # TODO this is kind of hacky, find a better way to handle this
@@ -2375,62 +2183,13 @@ async def inner_step(
                         f"[Mirix.Agent.{self.agent_state.name}] ERROR: Function execution encountered errors (see logs above for details)"
                     )
 
-            # if function_failed:
-
-            #     inputs = self._get_ai_reply(
-            #         message_sequence=input_message_sequence,
-            #         first_message=first_message,
-            #         stream=stream,
-            #         step_count=step_count,
-            #         # extra_messages=extra_messages,
-            #         get_input_data_for_debugging=True
-            #     )
-
-            #     try:
-            #         error = json.loads(all_response_messages[-1].content[0].text)
-            #     except:
-            #         error = 'Not Known'
-
-            #     response_json = response.model_dump()
-            #     response_json.pop('created', None)
-            #     results_to_log = {
-            #         'input': inputs,
-            #         'output': response_json,
-            #         'error': error
-            #     }
-
-            #     if not os.path.exists("debug"):
-            #         os.makedirs("debug")
-            #     count = 0
-            #     while os.path.exists(f"debug/debug_{count}.json"):
-            #         count += 1
-            #     with open(f"debug/debug_{count}.json", "w") as f:
-            #         json.dump(results_to_log, f, indent=2)
-
             # Step 6: extend the message history
             if len(messages) > 0:
                 all_new_messages = messages + all_response_messages
             else:
                 all_new_messages = all_response_messages
 
-            # Check the memory pressure and potentially issue a memory pressure warning
-            current_total_tokens = response.usage.total_tokens
-            active_memory_warning = False
-
-            # We can't do summarize logic properly if context_window is undefined
-            if self.agent_state.llm_config.context_window is None:
-                # Fallback if for some reason context_window is missing, just set to the default
-                printv(
-                    f"[Mirix.Agent.{self.agent_state.name}] WARNING: Could not find context_window in config, setting to default {LLM_MAX_TOKENS['DEFAULT']}"
-                )
-                printv(f"[Mirix.Agent.{self.agent_state.name}] DEBUG: Agent state: {self.agent_state}")
-                self.agent_state.llm_config.context_window = (
-                    LLM_MAX_TOKENS[self.model]
-                    if (self.model is not None and self.model in LLM_MAX_TOKENS)
-                    else LLM_MAX_TOKENS["DEFAULT"]
-                )
-
-            # Log step - this must happen before messages are persisted
+            # Log step
             step = await self.step_manager.log_step(
                 actor=self.actor,
                 provider_name=self.agent_state.llm_config.model_endpoint_type,
@@ -2441,36 +2200,6 @@ async def inner_step(
             for message in all_new_messages:
                 message.step_id = step.id
 
-            # Persisting into Messages - MUST happen before summarization
-            # so that summarize_messages_inplace can see all messages
-            self.agent_state = await self.agent_manager.append_to_in_context_messages(
-                all_new_messages,
-                agent_id=self.agent_state.id,
-                actor=self.actor,
-                user_id=self.user_id,
-            )
-
-            # Check memory pressure AFTER messages are persisted
-            if current_total_tokens > summarizer_settings.memory_warning_threshold * int(
-                self.agent_state.llm_config.context_window
-            ):
-                printv(
-                    f"[Mirix.Agent.{self.agent_state.name}] INFO: Memory pressure detected: last response total_tokens ({current_total_tokens}) > {summarizer_settings.memory_warning_threshold * int(self.agent_state.llm_config.context_window)}"
-                )
-
-                # Only deliver the alert if we haven't already (this period)
-                if not self.agent_alerted_about_memory_pressure:
-                    active_memory_warning = True
-                    self.agent_alerted_about_memory_pressure = True  # it's up to the outer loop to handle this
-
-                # if it is too long then run summarization here.
-                await self.summarize_messages_inplace(existing_file_uris=existing_file_uris)
-
-            else:
-                printv(
-                    f"[Mirix.Agent.{self.agent_state.name}] DEBUG: Memory usage acceptable: last response total_tokens ({current_total_tokens}) < {summarizer_settings.memory_warning_threshold * int(self.agent_state.llm_config.context_window)}"
-                )
-
             # Log step completion and results
             printv(
                 f"[Mirix.Agent.{self.agent_state.name}] INFO: Agent step completed - continue_chaining: {continue_chaining}, function_failed: {function_failed}, messages_generated: {len(all_new_messages)}"
@@ -2480,69 +2209,72 @@ async def inner_step(
                 messages=all_new_messages,
                 continue_chaining=continue_chaining,
                 function_failed=function_failed,
-                in_context_memory_warning=active_memory_warning,
                 usage=response.usage,
             )
 
         except Exception as e:
-            printv(f"[Mirix.Agent.{self.agent_state.name}] ERROR: step() failed\nmessages = {messages}\nerror = {e}")
-
-            # If we got a context alert, try trimming the messages length, then try again
+            printv(
+                f"[Mirix.Agent.{self.agent_state.name}] ERROR: inner_step() failed\nmessages = {messages}\nerror = {e}"
+            )
             if is_context_overflow_error(e):
-                in_context_messages = await self.agent_manager.get_in_context_messages(
-                    agent_state=self.agent_state, actor=self.actor, user=self.user
-                )
+                num_accumulated = len(accumulated) + len(messages)
 
-                if summarize_attempt_count <= summarizer_settings.max_summarizer_retries:
+                # Attempt summarization recovery: summarize retained DB messages
+                # and retry once with a smaller context.
+                retained = accumulated[:retained_count] if retained_count > 0 else []
+                if retained and not _summarization_attempted:
                     printv(
-                        f"[Mirix.Agent.{self.agent_state.name}] WARNING: context window exceeded with limit {self.agent_state.llm_config.context_window}, attempting to summarize ({summarize_attempt_count}/{summarizer_settings.max_summarizer_retries}"
+                        f"[Mirix.Agent.{self.agent_state.name}] INFO: "
+                        f"Context overflow with {num_accumulated} messages — "
+                        f"attempting summarization of {len(retained)} retained messages"
                     )
-                    # A separate API call to run a summarizer
-                    await self.summarize_messages_inplace(existing_file_uris=existing_file_uris)
+                    try:
+                        summary_msg = await self.summarize_and_replace_retained_messages(retained, existing_file_uris)
+                    except Exception as summarize_err:
+                        printv(
+                            f"[Mirix.Agent.{self.agent_state.name}] ERROR: " f"Summarization failed: {summarize_err}"
+                        )
+                        raise ContextWindowExceededError(
+                            f"Context window exceeded for agent id={self.agent_state.id} "
+                            f"and summarization recovery failed: {summarize_err}",
+                            details={"num_in_context_messages": num_accumulated},
+                        ) from e
+
+                    chaining_outputs = accumulated[retained_count:]
+                    new_accumulated = [summary_msg] + chaining_outputs
 
-                    # Try step again
                     return await self.inner_step(
                         messages=messages,
-                        first_message=first_message,
-                        first_input_messge=first_input_messge,
-                        first_message_retry_limit=first_message_retry_limit,
-                        skip_verify=skip_verify,
+                        accumulated=new_accumulated,
                         stream=stream,
-                        metadata=metadata,
-                        summarize_attempt_count=summarize_attempt_count + 1,
+                        step_count=step_count,
                         force_response=force_response,
-                        extra_messages=extra_messages,
                         topics=topics,
                         retrieved_memories=retrieved_memories,
-                        chaining=chaining,
-                        message_queue=message_queue,
-                        initial_message_count=initial_message_count,
-                        return_memory_types_without_update=return_memory_types_without_update,
                         display_intermediate_message=display_intermediate_message,
                         request_user_confirmation=request_user_confirmation,
                         existing_file_uris=existing_file_uris,
+                        return_memory_types_without_update=return_memory_types_without_update,
+                        message_queue=message_queue,
+                        chaining=chaining,
                         llm_client=llm_client,
-                    )
-                else:
-                    err_msg = f"Ran summarizer {summarize_attempt_count - 1} times for agent id={self.agent_state.id}, but messages are still overflowing the context window."
-                    token_counts = (get_token_counts_for_messages(in_context_messages),)
-                    printv(f"[Mirix.Agent.{self.agent_state.name}] ERROR: {err_msg}")
-                    printv(
-                        f"[Mirix.Agent.{self.agent_state.name}] ERROR: num_in_context_messages: {len(self.agent_state.message_ids)}"
-                    )
-                    printv(f"[Mirix.Agent.{self.agent_state.name}] ERROR: token_counts: {token_counts}")
-                    raise ContextWindowExceededError(
-                        err_msg,
-                        details={
-                            "num_in_context_messages": len(self.agent_state.message_ids),
-                            "in_context_messages_text": [m.text for m in in_context_messages],
-                            "token_counts": token_counts,
-                        },
+                        retained_count=1,
+                        _summarization_attempted=True,
+                        **kwargs,
                     )
 
+                err_msg = (
+                    f"Context window exceeded for agent id={self.agent_state.id} "
+                    f"with {num_accumulated} in-context messages."
+                )
+                printv(f"[Mirix.Agent.{self.agent_state.name}] ERROR: {err_msg}")
+                raise ContextWindowExceededError(
+                    err_msg,
+                    details={"num_in_context_messages": num_accumulated},
+                )
             else:
                 printv(
-                    f"[Mirix.Agent.{self.agent_state.name}] ERROR: step() failed with an unrecognized exception: '{str(e)}'"
+                    f"[Mirix.Agent.{self.agent_state.name}] ERROR: inner_step() failed with an unrecognized exception: '{str(e)}'"
                 )
                 raise e
 
@@ -2583,107 +2315,6 @@ async def step_user_message(self, user_message_str: str, **kwargs) -> AgentStepR
 
         return await self.inner_step(messages=[user_message], **kwargs)
 
-    async def summarize_messages_inplace(self, existing_file_uris: Optional[List[str]] = None):
-        in_context_messages = await self.agent_manager.get_in_context_messages(
-            agent_state=self.agent_state, actor=self.actor, user=self.user
-        )
-        in_context_messages_openai = [m.to_openai_dict() for m in in_context_messages]
-        in_context_messages_openai_no_system = in_context_messages_openai[1:]
-        token_counts = get_token_counts_for_messages(in_context_messages)
-        logger.info("System message token count=%s", token_counts[0])
-        logger.info("token_counts_no_system=%s", token_counts[1:])
-
-        if in_context_messages_openai[0]["role"] != "system":
-            raise RuntimeError(
-                f"in_context_messages_openai[0] should be system (instead got {in_context_messages_openai[0]})"
-            )
-
-        # If at this point there's nothing to summarize, throw an error
-        if len(in_context_messages_openai_no_system) == 0:
-            raise ContextWindowExceededError(
-                "Not enough messages to compress for summarization",
-                details={
-                    "num_candidate_messages": len(in_context_messages_openai_no_system),
-                    "num_total_messages": len(in_context_messages_openai),
-                },
-            )
-
-        cutoff = calculate_summarizer_cutoff(
-            in_context_messages=in_context_messages,
-            token_counts=token_counts,
-            logger=self.logger,
-        )
-
-        message_sequence_to_summarize = in_context_messages[1:cutoff]  # do NOT get rid of the system message
-        self.logger.info(
-            f"Attempting to summarize {len(message_sequence_to_summarize)} messages of {len(in_context_messages)}"
-        )
-
-        # We can't do summarize logic properly if context_window is undefined
-        if self.agent_state.llm_config.context_window is None:
-            # Fallback if for some reason context_window is missing, just set to the default
-            self.logger.warning(
-                f"{CLI_WARNING_PREFIX}could not find context_window in config, setting to default {LLM_MAX_TOKENS['DEFAULT']}"
-            )
-            self.agent_state.llm_config.context_window = (
-                LLM_MAX_TOKENS[self.model]
-                if (self.model is not None and self.model in LLM_MAX_TOKENS)
-                else LLM_MAX_TOKENS["DEFAULT"]
-            )
-
-        summary = await summarize_messages(
-            agent_state=self.agent_state,
-            message_sequence_to_summarize=message_sequence_to_summarize,
-            existing_file_uris=existing_file_uris,
-        )
-        logger.info("Got summary: %s", summary)
-
-        # Metadata that's useful for the agent to see
-        all_time_message_count = await self.message_manager.size(
-            agent_id=self.agent_state.id, actor=self.actor, user_id=self.user_id
-        )
-        remaining_message_count = 1 + len(in_context_messages) - cutoff  # System + remaining
-        hidden_message_count = all_time_message_count - remaining_message_count
-        summary_message_count = len(message_sequence_to_summarize)
-        summary_message = package_summarize_message(
-            summary, summary_message_count, hidden_message_count, all_time_message_count
-        )
-        logger.info("Packaged into message: %s", summary_message)
-
-        prior_len = len(in_context_messages_openai)
-        self.agent_state = await self.agent_manager.trim_older_in_context_messages(
-            num=cutoff,
-            agent_id=self.agent_state.id,
-            actor=self.actor,
-            user_id=self.user_id,
-        )
-        packed_summary_message = {"role": "user", "content": summary_message}
-
-        # Prepend the summary
-        self.agent_state = await self.agent_manager.prepend_to_in_context_messages(
-            messages=[
-                Message.dict_to_message(
-                    agent_id=self.agent_state.id,
-                    model=self.model,
-                    openai_message_dict=packed_summary_message,
-                )
-            ],
-            agent_id=self.agent_state.id,
-            actor=self.actor,
-            user_id=self.user_id,
-        )
-
-        # reset alert
-        self.agent_alerted_about_memory_pressure = False
-        curr_in_context_messages = await self.agent_manager.get_in_context_messages(
-            agent_state=self.agent_state, actor=self.actor, user=self.user
-        )
-
-        self.logger.info(f"Ran summarizer, messages length {prior_len} -> {len(curr_in_context_messages)}")
-        self.logger.info(
-            f"Summarizer brought down total token count from {sum(token_counts)} -> {sum(get_token_counts_for_messages(curr_in_context_messages))}"
-        )
-
     def add_function(self, function_name: str) -> str:
         # TODO: refactor
         raise NotImplementedError
@@ -2699,128 +2330,6 @@ def migrate_embedding(self, embedding_config: EmbeddingConfig):
         # TODO: recall memory
         raise NotImplementedError()
 
-    async def get_context_window(self) -> ContextWindowOverview:
-        """Get the context window of the agent"""
-
-        system_prompt = self.agent_state.system  # TODO is this the current system or the initial system?
-        num_tokens_system = count_tokens(system_prompt)
-        core_memory = self.blocks_in_memory.compile() if self.blocks_in_memory else ""
-        num_tokens_core_memory = count_tokens(core_memory)
-
-        # Grab the in-context messages
-        # conversion of messages to OpenAI dict format, which is passed to the token counter
-        in_context_messages = await self.agent_manager.get_in_context_messages(
-            agent_state=self.agent_state, actor=self.actor, user=self.user
-        )
-        in_context_messages_openai = [m.to_openai_dict() for m in in_context_messages]
-
-        # Check if there's a summary message in the message queue
-        if (
-            len(in_context_messages) > 1
-            and in_context_messages[1].role == MessageRole.user
-            and isinstance(in_context_messages[1].text, str)
-            # TODO remove hardcoding
-            and "The following is a summary of the previous " in in_context_messages[1].text
-        ):
-            # Summary message exists
-            assert in_context_messages[1].text is not None
-            summary_memory = in_context_messages[1].text
-            num_tokens_summary_memory = count_tokens(in_context_messages[1].text)
-            # with a summary message, the real messages start at index 2
-            num_tokens_messages = (
-                num_tokens_from_messages(messages=in_context_messages_openai[2:], model=self.model)
-                if len(in_context_messages_openai) > 2
-                else 0
-            )
-
-        else:
-            summary_memory = None
-            num_tokens_summary_memory = 0
-            # with no summary message, the real messages start at index 1
-            num_tokens_messages = (
-                num_tokens_from_messages(messages=in_context_messages_openai[1:], model=self.model)
-                if len(in_context_messages_openai) > 1
-                else 0
-            )
-
-        message_manager_size = await self.message_manager.size(
-            actor=self.actor, agent_id=self.agent_state.id, user_id=self.user_id
-        )
-        external_memory_summary = compile_memory_metadata_block(
-            memory_edit_timestamp=get_utc_time(),
-            previous_message_count=await self.message_manager.size(
-                actor=self.actor, agent_id=self.agent_state.id, user_id=self.user_id
-            ),
-        )
-        num_tokens_external_memory_summary = count_tokens(external_memory_summary)
-
-        # tokens taken up by function definitions
-        agent_state_tool_jsons = [t.json_schema for t in self.agent_state.tools]
-        if agent_state_tool_jsons:
-            available_functions_definitions = [
-                ChatCompletionRequestTool(type="function", function=f) for f in agent_state_tool_jsons
-            ]
-            num_tokens_available_functions_definitions = num_tokens_from_functions(
-                functions=agent_state_tool_jsons, model=self.model
-            )
-        else:
-            available_functions_definitions = []
-            num_tokens_available_functions_definitions = 0
-
-        num_tokens_used_total = (
-            num_tokens_system  # system prompt
-            + num_tokens_available_functions_definitions  # function definitions
-            + num_tokens_core_memory  # core memory
-            + num_tokens_external_memory_summary  # metadata (statistics) about recall/archival
-            + num_tokens_summary_memory  # summary of ongoing conversation
-            + num_tokens_messages  # tokens taken by messages
-        )
-        assert isinstance(num_tokens_used_total, int)
-
-        return ContextWindowOverview(
-            # context window breakdown (in messages)
-            num_messages=len(in_context_messages),
-            num_recall_memory=message_manager_size,
-            num_tokens_external_memory_summary=num_tokens_external_memory_summary,
-            external_memory_summary=external_memory_summary,
-            # top-level information
-            context_window_size_max=self.agent_state.llm_config.context_window,
-            context_window_size_current=num_tokens_used_total,
-            # context window breakdown (in tokens)
-            num_tokens_system=num_tokens_system,
-            system_prompt=system_prompt,
-            num_tokens_core_memory=num_tokens_core_memory,
-            core_memory=core_memory,
-            num_tokens_summary_memory=num_tokens_summary_memory,
-            summary_memory=summary_memory,
-            num_tokens_messages=num_tokens_messages,
-            messages=in_context_messages,
-            # related to functions
-            num_tokens_functions_definitions=num_tokens_available_functions_definitions,
-            functions_definitions=available_functions_definitions,
-        )
-
-    async def count_tokens(self) -> int:
-        """Count the tokens in the current context window"""
-        context_window_breakdown = await self.get_context_window()
-        return context_window_breakdown.context_window_size_current
-
-
-async def save_agent(agent: Agent):
-    """Save agent to metadata store"""
-    agent_state = agent.agent_state
-
-    # TODO: move this to agent manager
-    # TODO: Completely strip out metadata
-    # convert to persisted model
-    agent_manager = AgentManager()
-    update_agent = UpdateAgent(
-        message_ids=agent_state.message_ids,
-        # TODO: Add this back in later
-        # tool_exec_environment_variables=agent_state.get_agent_env_vars_as_dict(),
-    )
-    await agent_manager.update_agent(agent_id=agent_state.id, agent_update=update_agent, actor=agent.actor)
-
 
 def strip_name_field_from_user_message(
     user_message_text: str,
diff --git a/mirix/agent/meta_agent.py b/mirix/agent/meta_agent.py
index 6392bd8bb..36a59d000 100644
--- a/mirix/agent/meta_agent.py
+++ b/mirix/agent/meta_agent.py
@@ -502,9 +502,7 @@ async def update_embedding_config(self, embedding_config: EmbeddingConfig):
 
         actor = None
         if self.client_id:
-            actor = await self.server.client_manager.get_client_by_id(
-                self.client_id
-            )
+            actor = await self.server.client_manager.get_client_by_id(self.client_id)
 
         for agent_state in self.memory_agent_states.get_all_agent_states_list():
             if agent_state is not None:
diff --git a/mirix/agent/temporary_message_accumulator.py b/mirix/agent/temporary_message_accumulator.py
index 2b6e86bef..0f30400ba 100644
--- a/mirix/agent/temporary_message_accumulator.py
+++ b/mirix/agent/temporary_message_accumulator.py
@@ -14,6 +14,8 @@
 from mirix.constants import CHAINING_FOR_MEMORY_UPDATE, CHAINING_FOR_META_AGENT
 from mirix.voice_utils import convert_base64_to_audio_segment, process_voice_files
 
+logger = logging.getLogger(__name__)
+
 
 def get_image_mime_type(image_path):
     """Get MIME type for image files."""
@@ -704,7 +706,9 @@ async def _cleanup_processed_content(self, ready_to_process, user_message_added)
                     for file_ref in item["image_uris"]:
                         if hasattr(file_ref, "name"):
                             try:
-                                await self.client.server.cloud_file_mapping_manager.set_processed(cloud_file_id=file_ref.name)
+                                await self.client.server.cloud_file_mapping_manager.set_processed(
+                                    cloud_file_id=file_ref.name
+                                )
                             except Exception:
                                 pass
 
diff --git a/mirix/agent/upload_manager.py b/mirix/agent/upload_manager.py
index f13be9bf2..2100bda40 100644
--- a/mirix/agent/upload_manager.py
+++ b/mirix/agent/upload_manager.py
@@ -39,9 +39,12 @@ async def _compress_image(self, image_path, quality=85, max_size=(1920, 1080)):
         if shutil.which("vipsthumbnail"):
             try:
                 process = await asyncio.create_subprocess_exec(
-                    "vipsthumbnail", image_path,
-                    "--size", f"{max_size[0]}x{max_size[1]}",
-                    "-o", f"{compressed_path}[Q={quality},optimize-coding,strip]",
+                    "vipsthumbnail",
+                    image_path,
+                    "--size",
+                    f"{max_size[0]}x{max_size[1]}",
+                    "-o",
+                    f"{compressed_path}[Q={quality},optimize-coding,strip]",
                     stdout=asyncio.subprocess.PIPE,
                     stderr=asyncio.subprocess.PIPE,
                 )
@@ -52,13 +55,15 @@ async def _compress_image(self, image_path, quality=85, max_size=(1920, 1080)):
 
                 logger.warning(
                     "vipsthumbnail failed for %s (rc=%d): %s",
-                    image_path, process.returncode,
+                    image_path,
+                    process.returncode,
                     stderr_bytes.decode() if stderr_bytes else "",
                 )
             except Exception as e:
                 logger.warning(
                     "vipsthumbnail error for %s: %s; falling back to Pillow",
-                    image_path, e,
+                    image_path,
+                    e,
                 )
 
         # Fallback: Pillow in a child process (still async, separate process)
@@ -74,7 +79,9 @@ async def _compress_image(self, image_path, quality=85, max_size=(1920, 1080)):
                 f"quality={quality},optimize=True)"
             )
             process = await asyncio.create_subprocess_exec(
-                sys.executable, "-c", script,
+                sys.executable,
+                "-c",
+                script,
                 stdout=asyncio.subprocess.PIPE,
                 stderr=asyncio.subprocess.PIPE,
             )
@@ -85,7 +92,8 @@ async def _compress_image(self, image_path, quality=85, max_size=(1920, 1080)):
 
             logger.error(
                 "Pillow subprocess failed for %s (rc=%d): %s",
-                image_path, process.returncode,
+                image_path,
+                process.returncode,
                 stderr_bytes.decode() if stderr_bytes else "",
             )
             return None
@@ -115,6 +123,7 @@ async def _upload_single_file(self, upload_uuid, filename, timestamp, compressed
             upload_file = compressed_file if compressed_file and os.path.exists(compressed_file) else filename
 
             import time
+
             upload_start_time = time.time()
             file_ref = await self.google_client.aio.files.upload(file=upload_file)
             upload_duration = time.time() - upload_start_time
@@ -215,6 +224,7 @@ async def wait_for_upload(self, placeholder, timeout=30):
             return placeholder
 
         import time
+
         start_time = time.time()
         while time.time() - start_time < timeout:
             upload_status = await self.get_upload_status(placeholder)
@@ -245,7 +255,7 @@ async def cleanup_resolved_upload(self, placeholder):
     async def get_upload_status_summary(self):
         """Get a summary of current upload statuses."""
         async with self._upload_lock:
-            summary = {}
+            summary: dict[str, int] = {}
             for uid, info in self._upload_status.items():
                 status = info.get("status", "unknown")
                 summary[status] = summary.get(status, 0) + 1
diff --git a/mirix/client/client.py b/mirix/client/client.py
index 82660183f..39abff944 100644
--- a/mirix/client/client.py
+++ b/mirix/client/client.py
@@ -59,7 +59,6 @@ async def create_agent(
         include_meta_memory_tools: Optional[bool] = False,
         metadata: Optional[Dict] = None,
         description: Optional[str] = None,
-        initial_message_sequence: Optional[List[Message]] = None,
         tags: Optional[List[str]] = None,
     ) -> AgentState:
         raise NotImplementedError
@@ -74,7 +73,6 @@ async def update_agent(
         metadata: Optional[Dict] = None,
         llm_config: Optional[LLMConfig] = None,
         embedding_config: Optional[EmbeddingConfig] = None,
-        message_ids: Optional[List[str]] = None,
         memory: Optional[Memory] = None,
         tags: Optional[List[str]] = None,
     ):
@@ -110,9 +108,6 @@ async def get_archival_memory_summary(self, agent_id: str) -> ArchivalMemorySumm
     async def get_recall_memory_summary(self, agent_id: str) -> RecallMemorySummary:
         raise NotImplementedError
 
-    async def get_in_context_messages(self, agent_id: str) -> List[Message]:
-        raise NotImplementedError
-
     async def send_message(
         self,
         message: str,
diff --git a/mirix/client/remote_client.py b/mirix/client/remote_client.py
index 200bbd78d..4f0e67d96 100644
--- a/mirix/client/remote_client.py
+++ b/mirix/client/remote_client.py
@@ -15,28 +15,23 @@
 from mirix.client.client import AbstractClient
 from mirix.constants import FUNCTION_RETURN_CHAR_LIMIT
 from mirix.log import get_logger
-from mirix.schemas.agent import AgentState, AgentType, CreateAgent, CreateMetaAgent
-from mirix.schemas.block import Block, BlockUpdate, CreateBlock, Human, Persona
+from mirix.schemas.agent import AgentState, AgentType
+from mirix.schemas.block import Block, Human, Persona
 from mirix.schemas.embedding_config import EmbeddingConfig
 from mirix.schemas.environment_variables import (
     SandboxEnvironmentVariable,
-    SandboxEnvironmentVariableCreate,
-    SandboxEnvironmentVariableUpdate,
 )
-from mirix.schemas.file import FileMetadata
 from mirix.schemas.llm_config import LLMConfig
 from mirix.schemas.memory import ArchivalMemorySummary, Memory, RecallMemorySummary
-from mirix.schemas.message import Message, MessageCreate
+from mirix.schemas.message import Message
 from mirix.schemas.mirix_response import MirixResponse
 from mirix.schemas.organization import Organization
 from mirix.schemas.sandbox_config import (
     E2BSandboxConfig,
     LocalSandboxConfig,
     SandboxConfig,
-    SandboxConfigCreate,
-    SandboxConfigUpdate,
 )
-from mirix.schemas.tool import Tool, ToolCreate, ToolUpdate
+from mirix.schemas.tool import Tool
 from mirix.schemas.tool_rule import BaseToolRule
 
 logger = get_logger(__name__)
@@ -103,7 +98,7 @@ async def handle_async_request(self, request: httpx.Request) -> httpx.Response:
                 last_exc = exc
                 if attempt == self._max_retries:
                     raise
-            delay = self._backoff_factor * (2 ** attempt)
+            delay = self._backoff_factor * (2**attempt)
             await asyncio.sleep(delay)
         raise last_exc  # type: ignore[misc]
 
@@ -349,9 +344,7 @@ async def create_or_get_user(
         if not (headers and "X-API-Key" in headers) and (org_id or self.org_id):
             request_data["org_id"] = org_id or self.org_id
 
-        response = await self._request(
-            "POST", "/users/create_or_get", json=request_data, headers=headers
-        )
+        response = await self._request("POST", "/users/create_or_get", json=request_data, headers=headers)
         if isinstance(response, dict) and "id" in response:
             if self.debug:
                 logger.debug("User ready: %s", response["id"])
@@ -408,9 +401,7 @@ async def _request(
             if json:
                 logger.debug("[MirixClient] Request body: %s", json)
 
-        response = await self._client.request(
-            method=method, url=url, json=json, params=params, headers=headers
-        )
+        response = await self._client.request(method=method, url=url, json=json, params=params, headers=headers)
         try:
             response.raise_for_status()
         except httpx.HTTPStatusError as e:
@@ -418,9 +409,7 @@ async def _request(
                 error_detail = response.json().get("detail", str(e))
             except Exception:
                 error_detail = str(e)
-            raise httpx.HTTPStatusError(
-                error_detail, request=e.request, response=e.response
-            ) from e
+            raise httpx.HTTPStatusError(error_detail, request=e.request, response=e.response) from e
         if response.content:
             return response.json()
         return None
@@ -485,7 +474,6 @@ async def create_agent(
         include_meta_memory_tools: Optional[bool] = False,
         metadata: Optional[Dict] = None,
         description: Optional[str] = None,
-        initial_message_sequence: Optional[List[Message]] = None,
         tags: Optional[List[str]] = None,
         headers: Optional[Dict[str, str]] = None,
     ) -> AgentState:
@@ -504,9 +492,6 @@ async def create_agent(
             "include_meta_memory_tools": include_meta_memory_tools,
             "metadata": metadata,
             "description": description,
-            "initial_message_sequence": [
-                msg.model_dump() if hasattr(msg, "model_dump") else msg for msg in (initial_message_sequence or [])
-            ],
             "tags": tags,
         }
 
@@ -523,7 +508,6 @@ async def update_agent(
         metadata: Optional[Dict] = None,
         llm_config: Optional[LLMConfig] = None,
         embedding_config: Optional[EmbeddingConfig] = None,
-        message_ids: Optional[List[str]] = None,
         memory: Optional[Memory] = None,
         tags: Optional[List[str]] = None,
         headers: Optional[Dict[str, str]] = None,
@@ -537,7 +521,6 @@ async def update_agent(
             "metadata": metadata,
             "llm_config": llm_config.model_dump() if llm_config else None,
             "embedding_config": (embedding_config.model_dump() if embedding_config else None),
-            "message_ids": message_ids,
             "memory": memory.model_dump() if memory else None,
             "tags": tags,
         }
@@ -554,8 +537,7 @@ async def update_system_prompt(
         """
         Update an agent's system prompt by agent name.
 
-        This method updates the agent's system prompt and triggers a rebuild
-        of the system message in the agent's message history.
+        This method updates the agent's system prompt in persisted agent state.
 
         The method accepts short agent names like "episodic", "semantic", "core",
         or full names like "meta_memory_agent_episodic_memory_agent".
@@ -564,8 +546,6 @@ async def update_system_prompt(
         1. Resolves the agent name to agent_id for the authenticated client
         2. Updates the agent.system field in PostgreSQL
         3. Updates the agent.system field in Redis cache
-        4. Creates a new system message
-        5. Updates message_ids[0] to reference the new system message
 
         Args:
             agent_name: Name of the agent to update. Can be:
@@ -671,15 +651,13 @@ async def get_archival_memory_summary(
         data = await self._request("GET", f"/agents/{agent_id}/memory/archival", headers=headers)
         return ArchivalMemorySummary(**data)
 
-    async def get_recall_memory_summary(self, agent_id: str, headers: Optional[Dict[str, str]] = None) -> RecallMemorySummary:
+    async def get_recall_memory_summary(
+        self, agent_id: str, headers: Optional[Dict[str, str]] = None
+    ) -> RecallMemorySummary:
         """Get recall memory summary."""
         data = await self._request("GET", f"/agents/{agent_id}/memory/recall", headers=headers)
         return RecallMemorySummary(**data)
 
-    async def get_in_context_messages(self, agent_id: str) -> List[Message]:
-        """Get in-context messages."""
-        raise NotImplementedError("get_in_context_messages not yet implemented in REST API")
-
     # ========================================================================
     # Message Methods
     # ========================================================================
@@ -771,9 +749,7 @@ async def send_message(
         if not use_cache:
             request_data["use_cache"] = use_cache
 
-        data = await self._request(
-            "POST", f"/agents/{resolved_agent_id}/messages", json=request_data, headers=headers
-        )
+        data = await self._request("POST", f"/agents/{resolved_agent_id}/messages", json=request_data, headers=headers)
         return MirixResponse(**data)
 
     async def user_message(
diff --git a/mirix/constants.py b/mirix/constants.py
index 1dfedd582..1534416dc 100644
--- a/mirix/constants.py
+++ b/mirix/constants.py
@@ -122,9 +122,9 @@
     "semantic_memory_update",
     "check_semantic_memory",
 ]
-CHAT_AGENT_TOOLS = []
+CHAT_AGENT_TOOLS: list[str] = []
 EXTRAS_TOOLS = ["web_search", "fetch_and_read_pdf"]
-MCP_TOOLS = []
+MCP_TOOLS: list[str] = []
 META_MEMORY_TOOLS = ["trigger_memory_update"]
 SEARCH_MEMORY_TOOLS = ["search_in_memory", "list_memory_within_timerange"]
 UNIVERSAL_MEMORY_TOOLS = [
@@ -229,11 +229,6 @@
 INNER_THOUGHTS_CLI_SYMBOL = "💭"
 ASSISTANT_MESSAGE_CLI_SYMBOL = "🤖"
 
-CLEAR_HISTORY_AFTER_MEMORY_UPDATE = os.getenv("CLEAR_HISTORY_AFTER_MEMORY_UPDATE", "true").lower() in (
-    "true",
-    "1",
-    "yes",
-)
 CALL_MEMORY_AGENT_IN_PARALLEL = os.getenv("CALL_MEMORY_AGENT_IN_PARALLEL", "false").lower() in ("true", "1", "yes")
 CHAINING_FOR_MEMORY_UPDATE = os.getenv("CHAINING_FOR_MEMORY_UPDATE", "false").lower() in ("true", "1", "yes")
 CHAINING_FOR_META_AGENT = os.getenv("CHAINING_FOR_META_AGENT", "true").lower() in (
diff --git a/mirix/database/filter_tags_query.py b/mirix/database/filter_tags_query.py
index 775eeb055..41d655e9a 100644
--- a/mirix/database/filter_tags_query.py
+++ b/mirix/database/filter_tags_query.py
@@ -17,11 +17,10 @@
 
 import json
 import re
-from typing import Any, Dict, List, Optional, Tuple, Type
+from typing import Any, Dict, List, Optional, Tuple
 
 from sqlalchemy import cast, or_, text, type_coerce
 from sqlalchemy.dialects.postgresql import JSONB
-from sqlalchemy.orm import Query
 
 SUPPORTED_OPERATORS = frozenset({"$contains", "$exists", "$in"})
 
@@ -36,14 +35,12 @@ def _validate_operator(value: dict) -> str:
         )
     if len(ops) > 1:
         raise ValueError(
-            f"filter_tags value dict has multiple operator keys: {ops!r}. "
-            f"Only one operator per key is supported."
+            f"filter_tags value dict has multiple operator keys: {ops!r}. " f"Only one operator per key is supported."
         )
     op = ops[0]
     if op not in SUPPORTED_OPERATORS:
         raise ValueError(
-            f"Unknown filter_tags operator '{op}'. "
-            f"Supported operators: {', '.join(sorted(SUPPORTED_OPERATORS))}"
+            f"Unknown filter_tags operator '{op}'. " f"Supported operators: {', '.join(sorted(SUPPORTED_OPERATORS))}"
         )
     return op
 
@@ -94,9 +91,7 @@ def apply_filter_tags_sqlalchemy(
         if _is_operator_dict(value):
             query = query.where(_resolve_operator_sqla(key, value, model_class))
         else:
-            query = query.where(
-                model_class.filter_tags[key].as_string() == str(value)
-            )
+            query = query.where(model_class.filter_tags[key].as_string() == str(value))
 
     return query
 
@@ -104,10 +99,7 @@ def apply_filter_tags_sqlalchemy(
 def _apply_scopes_sqla(query, model_class, scopes: List[str]):
     """Apply scope authorization filter for SQLAlchemy."""
     if scopes:
-        scope_conditions = [
-            model_class.filter_tags["scope"].as_string() == scope
-            for scope in scopes
-        ]
+        scope_conditions = [model_class.filter_tags["scope"].as_string() == scope for scope in scopes]
         return query.where(or_(*scope_conditions))
     return query.where(text("1 = 0"))
 
@@ -119,9 +111,7 @@ def _resolve_operator_sqla(key: str, value: dict, model_class):
     if op == "$contains":
         # Pass the dict directly — type_coerce lets psycopg2 serialize it once.
         # Using json.dumps + cast would double-encode the string.
-        return cast(model_class.filter_tags, JSONB).contains(
-            type_coerce({key: [value["$contains"]]}, JSONB)
-        )
+        return cast(model_class.filter_tags, JSONB).contains(type_coerce({key: [value["$contains"]]}, JSONB))
     elif op == "$exists":
         condition = cast(model_class.filter_tags, JSONB).has_key(key)  # noqa: W601
         if not value["$exists"]:
@@ -131,15 +121,14 @@ def _resolve_operator_sqla(key: str, value: dict, model_class):
         vals = value["$in"]
         if not isinstance(vals, list) or not vals:
             return text("1 = 0")
-        return model_class.filter_tags[key].as_string().in_(
-            [str(v) for v in vals]
-        )
+        return model_class.filter_tags[key].as_string().in_([str(v) for v in vals])
 
 
 # ---------------------------------------------------------------------------
 # Raw SQL builder (for BM25 full-text search paths)
 # ---------------------------------------------------------------------------
 
+
 def build_filter_tags_raw_sql(
     filter_tags: Optional[Dict[str, Any]],
     scopes: Optional[List[str]] = None,
@@ -189,9 +178,7 @@ def _build_scopes_raw_sql(scopes: List[str]) -> Tuple[List[str], Dict[str, Any]]
 
     if scopes:
         placeholders = [f":scope_{i}" for i in range(len(scopes))]
-        clauses.append(
-            f"filter_tags->>'scope' IN ({', '.join(placeholders)})"
-        )
+        clauses.append(f"filter_tags->>'scope' IN ({', '.join(placeholders)})")
         for i, scope in enumerate(scopes):
             params[f"scope_{i}"] = scope
     else:
@@ -200,9 +187,7 @@ def _build_scopes_raw_sql(scopes: List[str]) -> Tuple[List[str], Dict[str, Any]]
     return clauses, params
 
 
-def _resolve_operator_raw_sql(
-    key: str, value: dict
-) -> Tuple[str, Dict[str, Any]]:
+def _resolve_operator_raw_sql(key: str, value: dict) -> Tuple[str, Dict[str, Any]]:
     """Resolve a single $ operator into a raw SQL clause + params."""
     op = _validate_operator(value)
     params: Dict[str, Any] = {}
@@ -237,6 +222,7 @@ def _resolve_operator_raw_sql(
 # Redis support
 # ---------------------------------------------------------------------------
 
+
 def can_redis_handle(filter_tags: Optional[Dict[str, Any]]) -> bool:
     """
     Check whether all filter_tags values can be handled by Redis TAG queries.
@@ -274,6 +260,7 @@ def build_filter_tags_redis(
     Callers should check can_redis_handle() first; this function only
     handles scalar values and scopes.
     """
+
     def escape_tag_value(val: str) -> str:
         special_chars = r'[\-:.()\[\]{}"\',<>;!@#$%^&*+=~]'
         return re.sub(special_chars, lambda m: f"\\{m.group(0)}", str(val))
diff --git a/mirix/database/redis_client.py b/mirix/database/redis_client.py
index 8b47325dc..ef4aa5aa1 100644
--- a/mirix/database/redis_client.py
+++ b/mirix/database/redis_client.py
@@ -853,9 +853,7 @@ async def delete(self, key: str) -> bool:
             logger.error("Failed to delete key %s: %s", key, e)
             return False
 
-    def _build_filter_tags_query(
-        self, filter_tags: Dict[str, Any], scopes: Optional[List[str]] = None
-    ) -> str:
+    def _build_filter_tags_query(self, filter_tags: Dict[str, Any], scopes: Optional[List[str]] = None) -> str:
         """
         Build Redis Search query string from filter_tags and scopes.
 
@@ -924,7 +922,6 @@ async def search_text(
                 return []
 
             import re
-            from datetime import datetime
 
             from redis.commands.search.query import Query
 
@@ -1057,8 +1054,6 @@ async def search_vector(
                 logger.debug("filter_tags contain operators unsupported by Redis, skipping Redis search_vector")
                 return []
 
-            from datetime import datetime
-
             import numpy as np
             from redis.commands.search.query import Query
 
@@ -1191,8 +1186,6 @@ async def search_recent(
                 logger.debug("filter_tags contain operators unsupported by Redis, skipping Redis search_recent")
                 return []
 
-            from datetime import datetime
-
             from redis.commands.search.query import Query
 
             # Build query parts
@@ -1294,7 +1287,6 @@ async def search_recent_by_org(
                 return []
 
             import re
-            from datetime import datetime
 
             from redis.commands.search.query import Query
 
@@ -1386,7 +1378,6 @@ async def search_vector_by_org(
                 return []
 
             import re
-            from datetime import datetime
 
             from redis.commands.search.query import Query
 
@@ -1480,7 +1471,6 @@ async def search_text_by_org(
                 return []
 
             import re
-            from datetime import datetime
 
             from redis.commands.search.query import Query
 
diff --git a/mirix/functions/function_sets/memory_tools.py b/mirix/functions/function_sets/memory_tools.py
index 8ce5a8f86..feb347edf 100644
--- a/mirix/functions/function_sets/memory_tools.py
+++ b/mirix/functions/function_sets/memory_tools.py
@@ -1,10 +1,9 @@
 import asyncio
-import os
 import re
 from copy import deepcopy
 from typing import TYPE_CHECKING, List, Optional
 
-from mirix.agent import Agent, AgentState
+from mirix.agent import Agent
 
 if TYPE_CHECKING:
     from mirix.schemas.memory import Memory
@@ -265,7 +264,9 @@ async def check_episodic_memory(self: "Agent", event_ids: List[str], timezone_st
         raise ValueError("User is required to check episodic memory")
 
     episodic_memory = [
-        await self.episodic_memory_manager.get_episodic_memory_by_id(event_id, user=self.user, timezone_str=timezone_str)
+        await self.episodic_memory_manager.get_episodic_memory_by_id(
+            event_id, user=self.user, timezone_str=timezone_str
+        )
         for event_id in event_ids
     ]
 
@@ -893,9 +894,7 @@ async def trigger_memory_update(self: "Agent", user_message: object, memory_type
     def _agent_type_key(at):
         return at.value if hasattr(at, "value") else str(at)
 
-    agent_type_to_state = {
-        _agent_type_key(agent_state.agent_type): agent_state for agent_state in child_agent_states
-    }
+    agent_type_to_state = {_agent_type_key(agent_state.agent_type): agent_state for agent_state in child_agent_states}
 
     if not child_agent_states:
         raise ValueError(
diff --git a/mirix/functions/helpers.py b/mirix/functions/helpers.py
index 1d07e1024..a8a31fc58 100755
--- a/mirix/functions/helpers.py
+++ b/mirix/functions/helpers.py
@@ -15,8 +15,6 @@
 from mirix.log import get_logger
 from mirix.schemas.enums import MessageRole
 from mirix.schemas.message import MessageCreate
-
-logger = get_logger(__name__)
 from mirix.schemas.mirix_message import (
     AssistantMessage,
     ReasoningMessage,
@@ -24,6 +22,8 @@
 )
 from mirix.schemas.mirix_response import MirixResponse
 
+logger = get_logger(__name__)
+
 if TYPE_CHECKING:
     try:
         from langchain_core.tools import BaseTool as LangChainBaseTool
diff --git a/mirix/functions/mcp_client/base_client.py b/mirix/functions/mcp_client/base_client.py
index fc4aee9a3..1c3aeeaac 100644
--- a/mirix/functions/mcp_client/base_client.py
+++ b/mirix/functions/mcp_client/base_client.py
@@ -12,7 +12,7 @@
 from mirix.observability.context import get_trace_context
 from mirix.observability.langfuse_client import get_langfuse_client
 
-from .exceptions import MCPConnectionError, MCPNotInitializedError, MCPTimeoutError
+from .exceptions import MCPConnectionError, MCPNotInitializedError
 from .types import BaseServerConfig, MCPTool
 
 logger = logging.getLogger(__name__)
diff --git a/mirix/functions/mcp_client/gmail_client.py b/mirix/functions/mcp_client/gmail_client.py
index 9bc22de6f..3c92e3df1 100644
--- a/mirix/functions/mcp_client/gmail_client.py
+++ b/mirix/functions/mcp_client/gmail_client.py
@@ -28,9 +28,7 @@
 ]
 
 
-def authenticate_gmail_local(
-    client_id: str, client_secret: str, token_file: str = None
-) -> dict:
+def authenticate_gmail_local(client_id: str, client_secret: str, token_file: str = None) -> dict:
     """
     Authenticate with Gmail using OAuth2 with a local server to catch the callback.
     This is an interactive browser-based flow; inherently sync.
@@ -66,9 +64,7 @@ def authenticate_gmail_local(
                         "client_secret": client_secret,
                         "auth_uri": "https://accounts.google.com/o/oauth2/auth",
                         "token_uri": "https://oauth2.googleapis.com/token",
-                        "auth_provider_x509_cert_url": (
-                            "https://www.googleapis.com/oauth2/v1/certs"
-                        ),
+                        "auth_provider_x509_cert_url": ("https://www.googleapis.com/oauth2/v1/certs"),
                         "redirect_uris": [
                             "http://localhost:8080/",
                             "http://localhost:8081/",
@@ -134,9 +130,7 @@ def _load_credentials(self) -> bool:
             with open(self._token_file) as f:
                 token_data = json.load(f)
             if not token_data.get("refresh_token"):
-                logger.warning(
-                    "Token file missing refresh_token, removing invalid token."
-                )
+                logger.warning("Token file missing refresh_token, removing invalid token.")
                 os.remove(self._token_file)
                 return False
 
@@ -145,9 +139,7 @@ def _load_credentials(self) -> bool:
                 refresh_token=token_data.get("refresh_token"),
                 expires_at=token_data.get("expiry"),
                 scopes=GMAIL_SCOPES,
-                token_uri=token_data.get(
-                    "token_uri", "https://oauth2.googleapis.com/token"
-                ),
+                token_uri=token_data.get("token_uri", "https://oauth2.googleapis.com/token"),
             )
             self._client_creds = ClientCreds(
                 client_id=self._client_id,
@@ -161,9 +153,7 @@ def _load_credentials(self) -> bool:
     async def _initialize_connection(self, server_config, timeout: float) -> bool:
         """Initialize Gmail connection using OAuth and discover the API."""
         try:
-            self._token_file = server_config.token_file or os.path.expanduser(
-                "~/.mirix/gmail_token.json"
-            )
+            self._token_file = server_config.token_file or os.path.expanduser("~/.mirix/gmail_token.json")
             self._client_id = server_config.client_id
             self._client_secret = server_config.client_secret
 
@@ -182,14 +172,10 @@ async def _initialize_connection(self, server_config, timeout: float) -> bool:
                     return False
 
                 if not self._load_credentials():
-                    logger.error(
-                        "Failed to load credentials after authentication"
-                    )
+                    logger.error("Failed to load credentials after authentication")
                     return False
 
-            async with Aiogoogle(
-                user_creds=self._user_creds, client_creds=self._client_creds
-            ) as aiogoogle:
+            async with Aiogoogle(user_creds=self._user_creds, client_creds=self._client_creds) as aiogoogle:
                 self._gmail_api = await aiogoogle.discover("gmail", "v1")
 
             logger.info("Gmail service initialized successfully")
@@ -201,9 +187,7 @@ async def _initialize_connection(self, server_config, timeout: float) -> bool:
 
     async def _execute_gmail_request(self, request):
         """Execute a single Gmail API request with auto token refresh."""
-        async with Aiogoogle(
-            user_creds=self._user_creds, client_creds=self._client_creds
-        ) as aiogoogle:
+        async with Aiogoogle(user_creds=self._user_creds, client_creds=self._client_creds) as aiogoogle:
             return await aiogoogle.as_user(request)
 
     async def list_tools(self) -> List[MCPTool]:
@@ -258,15 +242,11 @@ async def list_tools(self) -> List[MCPTool]:
                     "properties": {
                         "query": {
                             "type": "string",
-                            "description": (
-                                "Gmail search query (optional, e.g., 'is:unread')"
-                            ),
+                            "description": ("Gmail search query (optional, e.g., 'is:unread')"),
                         },
                         "max_results": {
                             "type": "integer",
-                            "description": (
-                                "Maximum number of emails to retrieve (default: 10)"
-                            ),
+                            "description": ("Maximum number of emails to retrieve (default: 10)"),
                             "default": 10,
                         },
                     },
@@ -288,16 +268,13 @@ async def list_tools(self) -> List[MCPTool]:
             ),
         ]
 
-    async def execute_tool(
-        self, tool_name: str, tool_args: Dict[str, Any]
-    ) -> Tuple[str, bool]:
+    async def execute_tool(self, tool_name: str, tool_args: Dict[str, Any]) -> Tuple[str, bool]:
         """Execute a Gmail tool."""
         self._check_initialized()
 
         if not await self._ensure_gmail_service():
             return (
-                "Gmail authentication required. "
-                "Please run the Gmail connection process.",
+                "Gmail authentication required. " "Please run the Gmail connection process.",
                 True,
             )
 
@@ -320,9 +297,7 @@ async def _ensure_gmail_service(self) -> bool:
             return True
 
         try:
-            success = await self._initialize_connection(
-                self.server_config, timeout=30.0
-            )
+            success = await self._initialize_connection(self.server_config, timeout=30.0)
             if success and self._gmail_api is not None:
                 logger.info("Gmail service established successfully")
                 return True
@@ -344,15 +319,9 @@ async def _send_email(self, args: Dict[str, Any]) -> Tuple[str, bool]:
             html_body = args.get("html_body")
             attachments = args.get("attachments", [])
 
-            message = self._create_message(
-                to, subject, body, cc, bcc, attachments, html_body
-            )
+            message = self._create_message(to, subject, body, cc, bcc, attachments, html_body)
 
-            result = await self._execute_gmail_request(
-                self._gmail_api.users.messages.send(
-                    userId="me", json=message
-                )
-            )
+            result = await self._execute_gmail_request(self._gmail_api.users.messages.send(userId="me", json=message))
 
             return f"Email sent successfully! Message ID: {result['id']}", False
 
@@ -370,9 +339,7 @@ async def _read_emails(self, args: Dict[str, Any]) -> Tuple[str, bool]:
                 client_creds=self._client_creds,
             ) as aiogoogle:
                 results = await aiogoogle.as_user(
-                    self._gmail_api.users.messages.list(
-                        userId="me", q=query, maxResults=max_results
-                    )
+                    self._gmail_api.users.messages.list(userId="me", q=query, maxResults=max_results)
                 )
 
                 messages = results.get("messages", [])
@@ -381,35 +348,19 @@ async def _read_emails(self, args: Dict[str, Any]) -> Tuple[str, bool]:
 
                 email_details = []
                 for msg_entry in messages:
-                    msg = await aiogoogle.as_user(
-                        self._gmail_api.users.messages.get(
-                            userId="me", id=msg_entry["id"]
-                        )
-                    )
+                    msg = await aiogoogle.as_user(self._gmail_api.users.messages.get(userId="me", id=msg_entry["id"]))
 
                     headers = msg["payload"].get("headers", [])
                     subject = next(
-                        (
-                            h["value"]
-                            for h in headers
-                            if h["name"] == "Subject"
-                        ),
+                        (h["value"] for h in headers if h["name"] == "Subject"),
                         "No Subject",
                     )
                     sender = next(
-                        (
-                            h["value"]
-                            for h in headers
-                            if h["name"] == "From"
-                        ),
+                        (h["value"] for h in headers if h["name"] == "From"),
                         "Unknown Sender",
                     )
                     date = next(
-                        (
-                            h["value"]
-                            for h in headers
-                            if h["name"] == "Date"
-                        ),
+                        (h["value"] for h in headers if h["name"] == "Date"),
                         "Unknown Date",
                     )
 
@@ -432,9 +383,7 @@ async def _get_email(self, args: Dict[str, Any]) -> Tuple[str, bool]:
         try:
             email_id = args["email_id"]
 
-            message = await self._execute_gmail_request(
-                self._gmail_api.users.messages.get(userId="me", id=email_id)
-            )
+            message = await self._execute_gmail_request(self._gmail_api.users.messages.get(userId="me", id=email_id))
 
             headers = message["payload"].get("headers", [])
             subject = next(
@@ -477,18 +426,12 @@ def _create_message(
     ) -> dict:
         """Create an email message dict for the Gmail API."""
         if html_body or attachments:
-            message = MIMEMultipart(
-                "alternative" if html_body else "mixed"
-            )
+            message = MIMEMultipart("alternative" if html_body else "mixed")
         else:
             message = MIMEText(body)
             message["to"] = to
             message["subject"] = subject
-            return {
-                "raw": base64.urlsafe_b64encode(
-                    message.as_bytes()
-                ).decode()
-            }
+            return {"raw": base64.urlsafe_b64encode(message.as_bytes()).decode()}
 
         message["to"] = to
         message["subject"] = subject
@@ -525,13 +468,9 @@ def _create_message(
                     )
                     message.attach(attachment)
                 else:
-                    logger.warning(
-                        "Attachment file '%s' not found", file_path
-                    )
+                    logger.warning("Attachment file '%s' not found", file_path)
 
-        return {
-            "raw": base64.urlsafe_b64encode(message.as_bytes()).decode()
-        }
+        return {"raw": base64.urlsafe_b64encode(message.as_bytes()).decode()}
 
     def _extract_message_body(self, payload):
         """Extract message body from Gmail API payload."""
@@ -544,8 +483,6 @@ def _extract_message_body(self, payload):
                     body = base64.urlsafe_b64decode(data).decode("utf-8")
                     break
         elif payload["body"].get("data"):
-            body = base64.urlsafe_b64decode(
-                payload["body"]["data"]
-            ).decode("utf-8")
+            body = base64.urlsafe_b64decode(payload["body"]["data"]).decode("utf-8")
 
         return body
diff --git a/mirix/functions/mcp_client/manager.py b/mirix/functions/mcp_client/manager.py
index 798cd34a4..646ff4e81 100644
--- a/mirix/functions/mcp_client/manager.py
+++ b/mirix/functions/mcp_client/manager.py
@@ -169,9 +169,7 @@ async def list_tools(self, server_name: Optional[str] = None) -> Dict[str, List[
                     all_tools[name] = []
             return all_tools
 
-    async def execute_tool(
-        self, server_name: str, tool_name: str, tool_args: Dict[str, Any]
-    ) -> Tuple[str, bool]:
+    async def execute_tool(self, server_name: str, tool_name: str, tool_args: Dict[str, Any]) -> Tuple[str, bool]:
         """Asynchronously execute a tool on a specific server"""
         await self._ensure_loaded()
 
@@ -194,9 +192,7 @@ async def find_tool(self, tool_name: str) -> Optional[Tuple[str, MCPTool]]:
                 logger.error(f"Failed to search tools in server {server_name}: {str(e)}")
         return None
 
-    async def execute_tool_by_name(
-        self, tool_name: str, tool_args: Dict[str, Any]
-    ) -> Tuple[str, bool]:
+    async def execute_tool_by_name(self, tool_name: str, tool_args: Dict[str, Any]) -> Tuple[str, bool]:
         """Execute a tool by name (searches all servers)"""
         result = await self.find_tool(tool_name)
         if result:
diff --git a/mirix/llm_api/anthropic_client.py b/mirix/llm_api/anthropic_client.py
index 612dc28de..26c9ac527 100644
--- a/mirix/llm_api/anthropic_client.py
+++ b/mirix/llm_api/anthropic_client.py
@@ -49,9 +49,7 @@
 class AnthropicClient(LLMClientBase):
     async def request(self, request_data: dict) -> dict:
         client = await self._get_anthropic_client(async_client=True)
-        response = await client.beta.messages.create(
-            **request_data, betas=["tools-2024-04-04"]
-        )
+        response = await client.beta.messages.create(**request_data, betas=["tools-2024-04-04"])
         return response.model_dump()
 
     @trace_method
@@ -112,7 +110,9 @@ async def send_llm_batch_request_async(
             raise self.handle_llm_error(e)
 
     @trace_method
-    async def _get_anthropic_client(self, async_client: bool = False) -> Union[anthropic.AsyncAnthropic, anthropic.Anthropic]:
+    async def _get_anthropic_client(
+        self, async_client: bool = False
+    ) -> Union[anthropic.AsyncAnthropic, anthropic.Anthropic]:
         override_key = await ProviderManager().get_anthropic_override_key()
         if async_client:
             return anthropic.AsyncAnthropic(api_key=override_key) if override_key else anthropic.AsyncAnthropic()
diff --git a/mirix/llm_api/azure_openai.py b/mirix/llm_api/azure_openai.py
index 5f455cc4f..4cda94d2e 100755
--- a/mirix/llm_api/azure_openai.py
+++ b/mirix/llm_api/azure_openai.py
@@ -29,9 +29,7 @@ def get_azure_deployment_list_endpoint(base_url: str):
     return f"{base_url}/openai/deployments?api-version=2023-03-15-preview"
 
 
-async def azure_openai_get_deployed_model_list(
-    base_url: str, api_key: str, api_version: str
-) -> List[dict]:
+async def azure_openai_get_deployed_model_list(base_url: str, api_key: str, api_version: str) -> List[dict]:
     """Returns list of deployed models using httpx."""
     headers = {"Content-Type": "application/json"}
     if api_key is not None:
@@ -65,9 +63,7 @@ async def azure_openai_get_deployed_model_list(
     return list(latest_models.values())
 
 
-async def azure_openai_get_chat_completion_model_list(
-    base_url: str, api_key: str, api_version: str
-) -> list:
+async def azure_openai_get_chat_completion_model_list(base_url: str, api_key: str, api_version: str) -> list:
     model_list = await azure_openai_get_deployed_model_list(base_url, api_key, api_version)
     # Extract models that support text generation
     model_options = [m for m in model_list if m.get("capabilities").get("chat_completion")]
diff --git a/mirix/llm_api/azure_openai_client.py b/mirix/llm_api/azure_openai_client.py
index c13d655d6..a11dfcc06 100644
--- a/mirix/llm_api/azure_openai_client.py
+++ b/mirix/llm_api/azure_openai_client.py
@@ -1,4 +1,3 @@
-
 import os
 from typing import List, Optional
 
@@ -104,9 +103,7 @@ async def request(self, request_data: dict) -> dict:
         Performs asynchronous request to Azure OpenAI API.
         """
         client = AsyncAzureOpenAI(**await self._prepare_client_kwargs())
-        response: ChatCompletion = await client.chat.completions.create(
-            **request_data
-        )
+        response: ChatCompletion = await client.chat.completions.create(**request_data)
         return response.model_dump()
 
     async def stream(self, request_data: dict) -> AsyncStream[ChatCompletionChunk]:
diff --git a/mirix/llm_api/google_ai.py b/mirix/llm_api/google_ai.py
index ee8a69bbc..6c17ea0fb 100644
--- a/mirix/llm_api/google_ai.py
+++ b/mirix/llm_api/google_ai.py
@@ -57,7 +57,9 @@ def get_gemini_endpoint_and_headers(
     return url, headers
 
 
-async def google_ai_get_model_details(base_url: str, api_key: str, model: str, key_in_header: bool = True) -> List[dict]:
+async def google_ai_get_model_details(
+    base_url: str, api_key: str, model: str, key_in_header: bool = True
+) -> List[dict]:
     from mirix.utils import printd
 
     url, headers = get_gemini_endpoint_and_headers(base_url, model, api_key, key_in_header)
@@ -93,7 +95,9 @@ async def google_ai_get_model_details(base_url: str, api_key: str, model: str, k
         raise e
 
 
-async def google_ai_get_model_context_window(base_url: str, api_key: str, model: str, key_in_header: bool = True) -> int:
+async def google_ai_get_model_context_window(
+    base_url: str, api_key: str, model: str, key_in_header: bool = True
+) -> int:
     model_details = await google_ai_get_model_details(
         base_url=base_url, api_key=api_key, model=model, key_in_header=key_in_header
     )
diff --git a/mirix/llm_api/google_ai_client.py b/mirix/llm_api/google_ai_client.py
index de40d53d8..4aa48f0a3 100644
--- a/mirix/llm_api/google_ai_client.py
+++ b/mirix/llm_api/google_ai_client.py
@@ -138,7 +138,9 @@ def combine_tool_responses(self, contents: List[dict]) -> List[dict]:
             idx += 1
         return new_contents
 
-    async def fill_image_content_in_messages(self, google_ai_message_list, existing_file_uris: Optional[List[str]] = None):
+    async def fill_image_content_in_messages(
+        self, google_ai_message_list, existing_file_uris: Optional[List[str]] = None
+    ):
         """
         Converts image URIs in the message to base64 format.
         """
@@ -549,7 +551,9 @@ async def google_ai_get_model_list(base_url: str, api_key: str, key_in_header: b
         raise e
 
 
-async def google_ai_get_model_details(base_url: str, api_key: str, model: str, key_in_header: bool = True) -> List[dict]:
+async def google_ai_get_model_details(
+    base_url: str, api_key: str, model: str, key_in_header: bool = True
+) -> List[dict]:
     from mirix.utils import printd
 
     url, headers = get_gemini_endpoint_and_headers(base_url, model, api_key, key_in_header)
@@ -579,7 +583,9 @@ async def google_ai_get_model_details(base_url: str, api_key: str, model: str, k
         raise e
 
 
-async def google_ai_get_model_context_window(base_url: str, api_key: str, model: str, key_in_header: bool = True) -> int:
+async def google_ai_get_model_context_window(
+    base_url: str, api_key: str, model: str, key_in_header: bool = True
+) -> int:
     model_details = await google_ai_get_model_details(
         base_url=base_url, api_key=api_key, model=model, key_in_header=key_in_header
     )
diff --git a/mirix/llm_api/helpers.py b/mirix/llm_api/helpers.py
index 153e86b79..7cecd8b45 100755
--- a/mirix/llm_api/helpers.py
+++ b/mirix/llm_api/helpers.py
@@ -1,18 +1,11 @@
-import copy
-import json
 import logging
-import warnings
-from collections import OrderedDict
 from typing import Any, List, Union
 
 import httpx
 
 from mirix.constants import OPENAI_CONTEXT_WINDOW_ERROR_SUBSTRING
-from mirix.schemas.enums import MessageRole
 from mirix.schemas.message import Message
-from mirix.schemas.openai.chat_completion_response import ChatCompletionResponse, Choice
-from mirix.settings import summarizer_settings
-from mirix.utils import count_tokens, json_dumps, printd
+from mirix.utils import count_tokens, printd
 
 logger = logging.getLogger(__name__)
 
@@ -191,64 +184,6 @@ async def make_post_request(url: str, headers: dict[str, str], data: dict[str, A
         raise Exception(error_message) from e
 
 
-def calculate_summarizer_cutoff(
-    in_context_messages: List[Message],
-    token_counts: List[int],
-    logger: "logging.Logger",
-) -> int:
-    if len(in_context_messages) != len(token_counts):
-        raise ValueError(
-            f"Given in_context_messages has different length from given token_counts: {len(in_context_messages)} != {len(token_counts)}"
-        )
-
-    in_context_messages_openai = [m.to_openai_dict() for m in in_context_messages]
-
-    if summarizer_settings.evict_all_messages:
-        logger.debug("Evicting all messages...")
-        return len(in_context_messages)
-    else:
-        # Start at index 1 (past the system message),
-        # and collect messages for summarization until we reach the desired truncation token fraction (eg 50%)
-        # We do the inverse of `desired_memory_token_pressure` to get what we need to remove
-        desired_token_count_to_summarize = int(
-            sum(token_counts) * (1 - summarizer_settings.desired_memory_token_pressure)
-        )
-        logger.debug(f"desired_token_count_to_summarize={desired_token_count_to_summarize}")
-
-        tokens_so_far = 0
-        cutoff = 0
-        for i, msg in enumerate(in_context_messages_openai):
-            # Skip system
-            if i == 0:
-                continue
-            cutoff = i
-            tokens_so_far += token_counts[i]
-
-            if msg["role"] not in ["user", "tool", "function"] and tokens_so_far >= desired_token_count_to_summarize:
-                # The intent of this code is to break on an assistant message boundary,
-                # so that we don't summarize in the middle of a back and forth turn.
-                # Break if the role is NOT a user or tool/function and tokens_so_far is enough
-                break
-            elif len(in_context_messages) - cutoff - 1 <= summarizer_settings.keep_last_n_messages:
-                # Also break if we reached the `keep_last_n_messages` threshold
-                # NOTE: This may be on a user, tool, or function in theory
-                logger.warning(
-                    f"Breaking summary cutoff early on role={msg['role']} because we hit the `keep_last_n_messages`={summarizer_settings.keep_last_n_messages}"
-                )
-                break
-        # If the next message is a tool call result, then include it in the set of messages to summarize as well.
-        # The intent of this code is so that tool calls and their results stay together. They are either both summarized
-        # or neither is.
-        while (
-            cutoff + 1 < len(in_context_messages_openai)
-            and in_context_messages_openai[cutoff + 1]["role"] == MessageRole.tool
-        ):
-            cutoff += 1
-
-        logger.debug("Evicting %s/%s messages...", cutoff, len(in_context_messages))
-        return cutoff + 1
-
-
 def get_token_counts_for_messages(in_context_messages: List[Message]) -> List[int]:
     in_context_messages_openai = [m.to_openai_dict() for m in in_context_messages]
     token_counts = [count_tokens(str(msg)) for msg in in_context_messages_openai]
diff --git a/mirix/llm_api/llm_api_tools.py b/mirix/llm_api/llm_api_tools.py
index ac4558042..4f086237a 100755
--- a/mirix/llm_api/llm_api_tools.py
+++ b/mirix/llm_api/llm_api_tools.py
@@ -6,15 +6,6 @@
 import httpx
 
 from mirix.constants import CLI_WARNING_PREFIX
-from mirix.log import get_logger
-from mirix.observability.context import get_trace_context, mark_observation_as_child
-from mirix.observability.langfuse_client import get_langfuse_client
-
-logger = get_logger(__name__)
-
-if TYPE_CHECKING:
-    from mirix.interface import AgentChunkStreamingInterface
-
 from mirix.errors import MirixConfigurationError, RateLimitExceededError
 from mirix.llm_api.anthropic import (
     anthropic_bedrock_chat_completions_request,
@@ -30,6 +21,9 @@
     build_openai_chat_completions_request,
     openai_chat_completions_request,
 )
+from mirix.log import get_logger
+from mirix.observability.context import get_trace_context, mark_observation_as_child
+from mirix.observability.langfuse_client import get_langfuse_client
 from mirix.schemas.llm_config import LLMConfig
 from mirix.schemas.message import Message
 from mirix.schemas.openai.chat_completion_request import (
@@ -41,6 +35,11 @@
 from mirix.settings import ModelSettings
 from mirix.utils import num_tokens_from_functions, num_tokens_from_messages
 
+logger = get_logger(__name__)
+
+if TYPE_CHECKING:
+    from mirix.interface import AgentChunkStreamingInterface
+
 LLM_API_PROVIDER_OPTIONS = [
     "openai",
     "azure",
@@ -203,9 +202,7 @@ async def create(
         try:
             messages_oai_format = [m.to_openai_dict() for m in messages]
             prompt_tokens = num_tokens_from_messages(messages=messages_oai_format, model=llm_config.model)
-            function_tokens = (
-                num_tokens_from_functions(functions=functions, model=llm_config.model) if functions else 0
-            )
+            function_tokens = num_tokens_from_functions(functions=functions, model=llm_config.model) if functions else 0
             if prompt_tokens + function_tokens > llm_config.context_window:
                 raise Exception(
                     f"Request exceeds maximum context length ({prompt_tokens + function_tokens} > {llm_config.context_window} tokens)"
@@ -272,13 +269,9 @@ async def create(
                                 if hasattr(msg, "tool_calls") and msg.tool_calls:
                                     output_message["tool_calls"] = [
                                         {
-                                            "name": (
-                                                tc.function.name if hasattr(tc, "function") else str(tc)
-                                            ),
+                                            "name": (tc.function.name if hasattr(tc, "function") else str(tc)),
                                             "arguments": (
-                                                str(tc.function.arguments)[:200]
-                                                if hasattr(tc, "function")
-                                                else ""
+                                                str(tc.function.arguments)[:200] if hasattr(tc, "function") else ""
                                             ),
                                         }
                                         for tc in msg.tool_calls[:5]
@@ -301,9 +294,7 @@ async def create(
             # azure
             elif llm_config.model_endpoint_type == "azure":
                 if stream:
-                    raise NotImplementedError(
-                        f"Streaming not yet implemented for {llm_config.model_endpoint_type}"
-                    )
+                    raise NotImplementedError(f"Streaming not yet implemented for {llm_config.model_endpoint_type}")
 
                 if model_settings.azure_api_key is None:
                     raise MirixConfigurationError(
@@ -344,9 +335,7 @@ async def create(
 
             elif llm_config.model_endpoint_type == "google_ai":
                 if stream:
-                    raise NotImplementedError(
-                        f"Streaming not yet implemented for {llm_config.model_endpoint_type}"
-                    )
+                    raise NotImplementedError(f"Streaming not yet implemented for {llm_config.model_endpoint_type}")
                 if not use_tool_naming:
                     raise NotImplementedError("Only tool calling supported on Google AI API requests")
 
@@ -442,9 +431,7 @@ async def create(
 
             elif llm_config.model_endpoint_type == "anthropic":
                 if stream:
-                    raise NotImplementedError(
-                        f"Streaming not yet implemented for {llm_config.model_endpoint_type}"
-                    )
+                    raise NotImplementedError(f"Streaming not yet implemented for {llm_config.model_endpoint_type}")
                 if not use_tool_naming:
                     raise NotImplementedError("Only tool calling supported on Anthropic API requests")
 
@@ -457,9 +444,7 @@ async def create(
                     data=ChatCompletionRequest(
                         model=llm_config.model,
                         messages=[cast_message_to_subtype(m.to_openai_dict()) for m in messages],
-                        tools=(
-                            [{"type": "function", "function": f} for f in functions] if functions else None
-                        ),
+                        tools=([{"type": "function", "function": f} for f in functions] if functions else None),
                         tool_choice=tool_call,
                         max_tokens=4096,  # TODO make dynamic
                         image_uris=image_uris["image_uris"],
@@ -481,17 +466,11 @@ async def create(
                         missing_fields=["groq_api_key"],
                     )
 
-                tools = (
-                    [{"type": "function", "function": f} for f in functions]
-                    if functions is not None
-                    else None
-                )
+                tools = [{"type": "function", "function": f} for f in functions] if functions is not None else None
                 data = ChatCompletionRequest(
                     model=llm_config.model,
                     messages=[
-                        m.to_openai_dict(
-                            put_inner_thoughts_in_kwargs=llm_config.put_inner_thoughts_in_kwargs
-                        )
+                        m.to_openai_dict(put_inner_thoughts_in_kwargs=llm_config.put_inner_thoughts_in_kwargs)
                         for m in messages
                     ],
                     tools=tools,
@@ -540,9 +519,7 @@ async def create(
                     data=ChatCompletionRequest(
                         model=llm_config.model,
                         messages=[cast_message_to_subtype(m.to_openai_dict()) for m in messages],
-                        tools=(
-                            [{"type": "function", "function": f} for f in functions] if functions else None
-                        ),
+                        tools=([{"type": "function", "function": f} for f in functions] if functions else None),
                         tool_choice=tool_call,
                         max_tokens=1024,  # TODO make dynamic
                     ),
diff --git a/mirix/llm_api/llm_client_base.py b/mirix/llm_api/llm_client_base.py
index bfce28254..09370ee9e 100644
--- a/mirix/llm_api/llm_client_base.py
+++ b/mirix/llm_api/llm_client_base.py
@@ -63,16 +63,12 @@ async def send_llm_request(
         trace_id = trace_context.get("trace_id") if trace_context else None
         parent_span_id = trace_context.get("observation_id") if trace_context else None
         if langfuse and trace_id:
-            return await self._execute_with_langfuse(
-                langfuse, request_data, messages, tools, trace_id, parent_span_id
-            )
+            return await self._execute_with_langfuse(langfuse, request_data, messages, tools, trace_id, parent_span_id)
         reason = "LangFuse client not available" if not langfuse else "No active trace_id in context"
         self.logger.debug(f"Sending LLM request without LangFuse tracing ({reason})")
         return await self._execute_without_langfuse(request_data, messages)
 
-    async def _execute_without_langfuse(
-        self, request_data: dict, messages: List[Message]
-    ) -> ChatCompletionResponse:
+    async def _execute_without_langfuse(self, request_data: dict, messages: List[Message]) -> ChatCompletionResponse:
         """Execute LLM request without LangFuse tracing."""
         try:
             t1 = time.time()
diff --git a/mirix/llm_api/openai_client.py b/mirix/llm_api/openai_client.py
index e0912103b..5696ff2da 100644
--- a/mirix/llm_api/openai_client.py
+++ b/mirix/llm_api/openai_client.py
@@ -1,4 +1,3 @@
-
 import base64
 import os
 from typing import List, Optional
@@ -293,9 +292,7 @@ async def request(self, request_data: dict) -> dict:
         Performs underlying asynchronous request to OpenAI API and returns raw response dict.
         """
         client_kwargs = await self._prepare_client_kwargs()
-        logger.debug(
-            "OpenAI Request - Making request to %s", client_kwargs.get("base_url")
-        )
+        logger.debug("OpenAI Request - Making request to %s", client_kwargs.get("base_url"))
         logger.debug(
             "OpenAI Request - Model: %s, Max tokens: %s, Temperature: %s",
             request_data.get("model"),
diff --git a/mirix/local_client/local_client.py b/mirix/local_client/local_client.py
index 995ab43ed..674dd9f58 100644
--- a/mirix/local_client/local_client.py
+++ b/mirix/local_client/local_client.py
@@ -14,7 +14,7 @@
 import os
 import shutil
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Union
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
 from urllib.parse import urlparse
 
 import httpx
@@ -175,9 +175,7 @@ async def _ensure_client(self) -> None:
         if self.organization is None:
             self.organization = await self.server.get_organization_or_default(self.org_id)
         if self.client is None:
-            self.client = await self.server.client_manager.get_client_or_default(
-                self.client_id, self.org_id
-            )
+            self.client = await self.server.client_manager.get_client_or_default(self.client_id, self.org_id)
 
     @classmethod
     async def create(
@@ -530,7 +528,6 @@ async def create_agent(
         # metadata
         metadata: Optional[Dict] = None,
         description: Optional[str] = None,
-        initial_message_sequence: Optional[List[Message]] = None,
         tags: Optional[List[str]] = None,
     ) -> AgentState:
         """Create an agent.
@@ -579,9 +576,7 @@ async def _resolve_tool_ids():
 
         memory = memory or Memory()
         for block in memory.get_blocks():
-            await self.server.block_manager.create_or_update_block(
-                block, actor=self.client, user=self.user
-            )
+            await self.server.block_manager.create_or_update_block(block, actor=self.client, user=self.user)
 
         block_ids = block_ids or []
         create_params = {
@@ -596,7 +591,6 @@ async def _resolve_tool_ids():
             "agent_type": agent_type,
             "llm_config": llm_config if llm_config else self._default_llm_config,
             "embedding_config": (embedding_config if embedding_config else self._default_embedding_config),
-            "initial_message_sequence": initial_message_sequence,
             "tags": tags,
         }
         if name is not None:
@@ -606,14 +600,10 @@ async def _resolve_tool_ids():
             CreateAgent(**create_params),
             actor=self.client,
         )
-        return await self.server.agent_manager.get_agent_by_id(
-            agent_state.id, actor=self.client
-        )
+        return await self.server.agent_manager.get_agent_by_id(agent_state.id, actor=self.client)
 
     async def create_user(self, user_id: str, user_name: str) -> PydanticUser:
-        return await self.server.user_manager.create_user(
-            UserCreate(id=user_id, name=user_name)
-        )
+        return await self.server.user_manager.create_user(UserCreate(id=user_id, name=user_name))
 
     async def create_meta_agent(
         self,
@@ -649,9 +639,7 @@ async def get_tools_from_agent(self, agent_id: str) -> List[Tool]:
         """Get tools from an existing agent."""
         self.interface.clear()
         await self._ensure_client()
-        agent = await self.server.agent_manager.get_agent_by_id(
-            agent_id=agent_id, actor=self.client
-        )
+        agent = await self.server.agent_manager.get_agent_by_id(agent_id=agent_id, actor=self.client)
         return agent.tools
 
     async def add_tool_to_agent(self, agent_id: str, tool_id: str) -> AgentState:
@@ -667,9 +655,7 @@ async def add_tool_to_agent(self, agent_id: str, tool_id: str) -> AgentState:
         """
         self.interface.clear()
         await self._ensure_client()
-        return await self.server.agent_manager.attach_tool(
-            agent_id=agent_id, tool_id=tool_id, actor=self.client
-        )
+        return await self.server.agent_manager.attach_tool(agent_id=agent_id, tool_id=tool_id, actor=self.client)
 
     async def remove_tool_from_agent(self, agent_id: str, tool_id: str) -> AgentState:
         """
@@ -684,9 +670,7 @@ async def remove_tool_from_agent(self, agent_id: str, tool_id: str) -> AgentStat
         """
         self.interface.clear()
         await self._ensure_client()
-        return await self.server.agent_manager.detach_tool(
-            agent_id=agent_id, tool_id=tool_id, actor=self.client
-        )
+        return await self.server.agent_manager.detach_tool(agent_id=agent_id, tool_id=tool_id, actor=self.client)
 
     async def update_agent(
         self,
@@ -698,7 +682,6 @@ async def update_agent(
         metadata: Optional[Dict] = None,
         llm_config: Optional[LLMConfig] = None,
         embedding_config: Optional[EmbeddingConfig] = None,
-        message_ids: Optional[List[str]] = None,
     ):
         """
         Update an agent's configuration.
@@ -712,7 +695,6 @@ async def update_agent(
             metadata (Dict): New metadata
             llm_config (LLMConfig): New LLM configuration
             embedding_config (EmbeddingConfig): New embedding configuration
-            message_ids (List[str]): New list of message IDs
 
         Returns:
             AgentState: Updated agent state
@@ -735,8 +717,6 @@ async def update_agent(
             update_data["llm_config"] = llm_config
         if embedding_config is not None:
             update_data["embedding_config"] = embedding_config
-        if message_ids is not None:
-            update_data["message_ids"] = message_ids
 
         agent_update = UpdateAgent(**update_data)
         await self._ensure_client()
@@ -757,17 +737,13 @@ async def get_agent_by_name(self, agent_name: str) -> AgentState:
         """Get an agent by its name."""
         self.interface.clear()
         await self._ensure_client()
-        return await self.server.agent_manager.get_agent_by_name(
-            agent_name=agent_name, actor=self.client
-        )
+        return await self.server.agent_manager.get_agent_by_name(agent_name=agent_name, actor=self.client)
 
     async def get_agent(self, agent_id: str) -> AgentState:
         """Get an agent's state by its ID."""
         self.interface.clear()
         await self._ensure_client()
-        return await self.server.agent_manager.get_agent_by_id(
-            agent_id=agent_id, actor=self.client
-        )
+        return await self.server.agent_manager.get_agent_by_id(agent_id=agent_id, actor=self.client)
 
     async def get_agent_id(self, agent_name: str) -> Optional[str]:
         """Get the ID of an agent by name (names are unique per user)."""
@@ -782,9 +758,7 @@ async def get_agent_id(self, agent_name: str) -> Optional[str]:
     async def get_archival_memory_summary(self, agent_id: str) -> ArchivalMemorySummary:
         """Get a summary of the archival memory of an agent."""
         await self._ensure_client()
-        return await self.server.get_archival_memory_summary(
-            agent_id=agent_id, actor=self.client
-        )
+        return await self.server.get_archival_memory_summary(agent_id=agent_id, actor=self.client)
 
     async def get_recall_memory_summary(self, agent_id: str) -> RecallMemorySummary:
         """Get a summary of the recall memory of an agent."""
@@ -794,31 +768,6 @@ async def get_recall_memory_summary(self, agent_id: str) -> RecallMemorySummary:
             actor=self.client,
         )
 
-    async def get_in_context_messages(self, agent_id: str, user_id: Optional[str] = None) -> List[Message]:
-        """
-        Get in-context messages of an agent
-
-        Args:
-            agent_id (str): ID of the agent
-            user_id (str): Optional user ID to filter messages for. If None, returns all messages.
-
-        Returns:
-            messages (List[Message]): List of in-context messages
-        """
-        await self._ensure_client()
-        agent_state = await self.server.agent_manager.get_agent_by_id(
-            agent_id=agent_id,
-            actor=self.client,
-        )
-        user = None
-        if user_id:
-            user = await self.server.user_manager.get_user_by_id(user_id)
-        return await self.server.agent_manager.get_in_context_messages(
-            agent_state=agent_state,
-            actor=self.client,
-            user=user,
-        )
-
     # agent interactions
 
     async def construct_system_message(self, agent_id: str, message: str, user_id: str) -> str:
@@ -832,9 +781,7 @@ async def construct_system_message(self, agent_id: str, message: str, user_id: s
             actor=self.client,
         )
 
-    async def extract_memory_for_system_prompt(
-        self, agent_id: str, message: str, user_id: Optional[str] = None
-    ) -> str:
+    async def extract_memory_for_system_prompt(self, agent_id: str, message: str, user_id: Optional[str] = None) -> str:
         """Extract memory for system prompt from a message."""
         await self._ensure_client()
         return await self.server.extract_memory_for_system_prompt(
@@ -1077,9 +1024,7 @@ async def convert_message(m):
     async def user_message(self, agent_id: str, message: str, user_id: Optional[str] = None) -> MirixResponse:
         """Send a message to an agent as a user."""
         self.interface.clear()
-        return await self.send_message(
-            role="user", agent_id=agent_id, message=message, user_id=user_id
-        )
+        return await self.send_message(role="user", agent_id=agent_id, message=message, user_id=user_id)
 
     async def run_command(self, agent_id: str, command: str) -> MirixResponse:
         """
@@ -1499,9 +1444,7 @@ async def list_tools(self, cursor: Optional[str] = None, limit: Optional[int] =
             List of tools.
         """
         await self._ensure_client()
-        return await self.server.tool_manager.list_tools(
-            cursor=cursor, limit=limit, actor=self.client
-        )
+        return await self.server.tool_manager.list_tools(cursor=cursor, limit=limit, actor=self.client)
 
     async def get_tool(self, id: str) -> Tool:
         """
@@ -1542,13 +1485,13 @@ async def get_tool_id(self, name: str) -> Optional[str]:
     async def get_tool_by_name(self, name: str) -> Optional[Tool]:
         """Get tool by name."""
         await self._ensure_client()
-        return await self.server.tool_manager.get_tool_by_name(
-            tool_name=name, actor=self.client
-        )
+        return await self.server.tool_manager.get_tool_by_name(tool_name=name, actor=self.client)
 
     # recall memory
 
-    async def get_messages(self, agent_id: str, cursor: Optional[str] = None, limit: Optional[int] = 1000) -> List[Message]:
+    async def get_messages(
+        self, agent_id: str, cursor: Optional[str] = None, limit: Optional[int] = 1000
+    ) -> List[Message]:
         """
         Get messages from an agent with pagination.
 
@@ -1778,9 +1721,7 @@ async def delete_file(self, file_id: str) -> None:
 
     async def search_files(self, name_pattern: str) -> List[FileMetadata]:
         """Search files by name pattern."""
-        return await self.file_manager.search_files_by_name(
-            file_name=name_pattern, organization_id=self.org_id
-        )
+        return await self.file_manager.search_files_by_name(file_name=name_pattern, organization_id=self.org_id)
 
     async def get_file_stats(self) -> dict:
         """
diff --git a/mirix/memory.py b/mirix/memory.py
index 0498041cc..0e1113b65 100755
--- a/mirix/memory.py
+++ b/mirix/memory.py
@@ -8,7 +8,6 @@
 from mirix.schemas.memory import Memory
 from mirix.schemas.message import Message
 from mirix.schemas.mirix_message_content import TextContent
-from mirix.settings import summarizer_settings
 from mirix.utils import count_tokens, printd
 
 
@@ -62,43 +61,37 @@ async def summarize_messages(
     agent_state: AgentState,
     message_sequence_to_summarize: List[Message],
     existing_file_uris: Optional[List[str]] = None,
-):
-    """Summarize a message sequence using GPT"""
-    # we need the context_window
+) -> str:
+    """Summarize a message sequence using the agent's LLM.
+
+    If the formatted input exceeds ~60% of the context window, the message
+    list is truncated (keeping the newest messages) so the summarizer call
+    itself doesn't overflow.
+    """
     context_window = agent_state.llm_config.context_window
+    max_input_tokens = int(context_window * 0.6)
 
-    summary_prompt = SUMMARY_PROMPT_SYSTEM
     summary_input = _format_summary_history(message_sequence_to_summarize)
     summary_input_tkns = count_tokens(summary_input)
-    if summary_input_tkns > summarizer_settings.memory_warning_threshold * context_window:
-        trunc_ratio = (
-            summarizer_settings.memory_warning_threshold * context_window / summary_input_tkns
-        ) * 0.8  # For good measure...
-        cutoff = int(len(message_sequence_to_summarize) * trunc_ratio)
-        summary_input = str(
-            [
-                await summarize_messages(
-                    agent_state,
-                    message_sequence_to_summarize=message_sequence_to_summarize[:cutoff],
-                )
-            ]
-            + message_sequence_to_summarize[cutoff:]
-        )
-
-    dummy_agent_id = agent_state.id
+
+    if summary_input_tkns > max_input_tokens:
+        ratio = max_input_tokens / summary_input_tkns * 0.8
+        keep = max(1, int(len(message_sequence_to_summarize) * ratio))
+        summary_input = _format_summary_history(message_sequence_to_summarize[-keep:])
+
     message_sequence = [
         Message(
-            agent_id=dummy_agent_id,
+            agent_id=agent_state.id,
             role=MessageRole.system,
-            content=[TextContent(text=summary_prompt)],
+            content=[TextContent(text=SUMMARY_PROMPT_SYSTEM)],
         ),
         Message(
-            agent_id=dummy_agent_id,
+            agent_id=agent_state.id,
             role=MessageRole.assistant,
             content=[TextContent(text=MESSAGE_SUMMARY_REQUEST_ACK)],
         ),
         Message(
-            agent_id=dummy_agent_id,
+            agent_id=agent_state.id,
             role=MessageRole.user,
             content=[TextContent(text=summary_input)],
         ),
@@ -114,5 +107,4 @@ async def summarize_messages(
     )
 
     printd(f"summarize_messages gpt reply: {response.choices[0]}")
-    reply = response.choices[0].message.content
-    return reply
+    return response.choices[0].message.content
diff --git a/mirix/orm/agent.py b/mirix/orm/agent.py
index 485cbecad..41d86435d 100755
--- a/mirix/orm/agent.py
+++ b/mirix/orm/agent.py
@@ -1,7 +1,7 @@
 import uuid
 from typing import TYPE_CHECKING, List, Optional
 
-from sqlalchemy import JSON, String
+from sqlalchemy import JSON, String  # JSON retained for mcp_tools column
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
 from mirix.orm.custom_columns import (
@@ -50,10 +50,6 @@ class Agent(SqlalchemyBase, OrganizationMixin):
     # System prompt
     system: Mapped[Optional[str]] = mapped_column(String, nullable=True, doc="The system prompt used by the agent.")
 
-    message_ids: Mapped[Optional[List[str]]] = mapped_column(
-        JSON, nullable=True, doc="List of message IDs in in-context memory."
-    )
-
     # Metadata and configs
     llm_config: Mapped[Optional[LLMConfig]] = mapped_column(
         LLMConfigColumn,
@@ -80,13 +76,27 @@ class Agent(SqlalchemyBase, OrganizationMixin):
     messages: Mapped[List["Message"]] = relationship(
         "Message",
         back_populates="agent",
-        lazy="selectin",
+        lazy="noload",
         cascade="all, delete-orphan",  # Ensure messages are deleted when the agent is deleted
         passive_deletes=True,
     )
 
     def to_pydantic(self) -> PydanticAgentState:
         """converts to the basic pydantic model counterpart"""
+        from sqlalchemy import inspect
+
+        # Check if we're in a session and tools are loaded
+        # This prevents MissingGreenlet when accessing relationships outside session
+        insp = inspect(self)
+
+        # For tools: if already loaded, use them; otherwise use empty list
+        # tools has lazy="selectin" so should be loaded, but this handles edge cases
+        if "tools" in insp.dict:
+            tools = self.tools
+        else:
+            # Tools not loaded (detached instance or session closed)
+            tools = []
+
         state = {
             "id": self.id,
             "organization_id": self.organization_id,
@@ -94,8 +104,7 @@ def to_pydantic(self) -> PydanticAgentState:
             "description": self.description,
             "parent_id": self.parent_id,
             "children": None,  # Children are populated separately when needed
-            "message_ids": self.message_ids,
-            "tools": self.tools,
+            "tools": tools,
             "tool_rules": self.tool_rules,
             "system": self.system,
             "agent_type": self.agent_type,
diff --git a/mirix/orm/base.py b/mirix/orm/base.py
index 3644640b1..5ab182cb0 100755
--- a/mirix/orm/base.py
+++ b/mirix/orm/base.py
@@ -1,5 +1,4 @@
-import datetime as dt
-from datetime import datetime
+from datetime import datetime, timezone
 from typing import Optional
 
 from sqlalchemy import Boolean, DateTime, String, func, text
@@ -34,7 +33,7 @@ def set_updated_at(self, timestamp: Optional[datetime] = None) -> None:
             timestamp (Optional[datetime]): The timestamp to set.
                                             If None, uses the current UTC time.
         """
-        self.updated_at = timestamp or datetime.now(dt.UTC)
+        self.updated_at = timestamp or datetime.now(timezone.utc)
 
     def _set_created_and_updated_by_fields(self, actor_id: str) -> None:
         """Populate created_by_id and last_updated_by_id based on actor."""
diff --git a/mirix/orm/block.py b/mirix/orm/block.py
index 399f5bd71..91fd21ac1 100755
--- a/mirix/orm/block.py
+++ b/mirix/orm/block.py
@@ -1,7 +1,6 @@
 from typing import TYPE_CHECKING, List, Optional, Type
 
-from sqlalchemy import JSON, BigInteger, Index, Integer, String, UniqueConstraint, cast, event, or_, select, text
-from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy import JSON, BigInteger, Index, Integer, UniqueConstraint, event, or_, select, text
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import (
     Mapped,
diff --git a/mirix/orm/client.py b/mirix/orm/client.py
index f306d1950..dec496d2e 100644
--- a/mirix/orm/client.py
+++ b/mirix/orm/client.py
@@ -29,6 +29,11 @@ class Client(SqlalchemyBase, OrganizationMixin):
         JSON, nullable=False, default=list, doc="Scopes for reading memories."
     )
 
+    # Message retention
+    message_set_retention_count: Mapped[Optional[int]] = mapped_column(
+        nullable=True, default=0, doc="Number of input message-sets to retain per (agent, user). 0 = no retention."
+    )
+
     # Dashboard authentication fields
     email: Mapped[Optional[str]] = mapped_column(
         nullable=True, unique=True, index=True, doc="Email address for dashboard login."
diff --git a/mirix/orm/custom_columns.py b/mirix/orm/custom_columns.py
index f51621662..3f66003f0 100755
--- a/mirix/orm/custom_columns.py
+++ b/mirix/orm/custom_columns.py
@@ -1,4 +1,4 @@
-from datetime import datetime, timezone
+from datetime import timezone
 
 from sqlalchemy import JSON
 from sqlalchemy.types import BINARY, DateTime, TypeDecorator
diff --git a/mirix/orm/episodic_memory.py b/mirix/orm/episodic_memory.py
index 341fcb1da..2928fd82f 100755
--- a/mirix/orm/episodic_memory.py
+++ b/mirix/orm/episodic_memory.py
@@ -204,3 +204,31 @@ def user(cls) -> Mapped["User"]:
         Relationship to the User that owns this episodic event.
         """
         return relationship("User", lazy="selectin")
+
+    def to_pydantic(self) -> PydanticEpisodicEvent:
+        """
+        Convert to Pydantic model, safely handling relationship loading.
+        This prevents MissingGreenlet errors when converting detached instances.
+        """
+        # Build dict with only scalar fields (no relationships)
+        # Pydantic model expects scalars only; relationships are foreign keys
+        state = {
+            "id": self.id,
+            "agent_id": self.agent_id,
+            "client_id": self.client_id,
+            "user_id": self.user_id,
+            "organization_id": self.organization_id,
+            "occurred_at": self.occurred_at,
+            "last_modify": self.last_modify,
+            "actor": self.actor,
+            "event_type": self.event_type,
+            "summary": self.summary,
+            "details": self.details,
+            "filter_tags": self.filter_tags,
+            "embedding_config": self.embedding_config,
+            "details_embedding": self.details_embedding,
+            "summary_embedding": self.summary_embedding,
+            "created_at": self.created_at,
+            "updated_at": self.updated_at,
+        }
+        return self.__pydantic_model__(**state)
diff --git a/mirix/orm/knowledge_vault.py b/mirix/orm/knowledge_vault.py
index d9e7279cf..8ebe69374 100755
--- a/mirix/orm/knowledge_vault.py
+++ b/mirix/orm/knowledge_vault.py
@@ -176,3 +176,28 @@ def user(cls) -> Mapped["User"]:
         Relationship to the User that owns this knowledge vault item.
         """
         return relationship("User", lazy="selectin")
+
+    def to_pydantic(self) -> "PydanticKnowledgeVaultItem":
+        """
+        Convert to Pydantic model, safely handling relationship loading.
+        This prevents MissingGreenlet errors when converting detached instances.
+        """
+        state = {
+            "id": self.id,
+            "agent_id": self.agent_id,
+            "client_id": self.client_id,
+            "user_id": self.user_id,
+            "organization_id": self.organization_id,
+            "entry_type": self.entry_type,
+            "source": self.source,
+            "sensitivity": self.sensitivity,
+            "secret_value": self.secret_value,
+            "caption": self.caption,
+            "filter_tags": self.filter_tags,
+            "last_modify": self.last_modify,
+            "embedding_config": self.embedding_config,
+            "caption_embedding": self.caption_embedding,
+            "created_at": self.created_at,
+            "updated_at": self.updated_at,
+        }
+        return self.__pydantic_model__(**state)
diff --git a/mirix/orm/message.py b/mirix/orm/message.py
index bab3fa91b..d0847adbe 100755
--- a/mirix/orm/message.py
+++ b/mirix/orm/message.py
@@ -32,6 +32,7 @@ class Message(SqlalchemyBase, OrganizationMixin, UserMixin, AgentMixin):
         Index("ix_messages_created_at", "created_at", "id"),
         Index("ix_messages_client_user", "client_id", "user_id"),
         Index("ix_messages_agent_client_user", "agent_id", "client_id", "user_id"),
+        Index("ix_messages_agent_user_created_at", "agent_id", "user_id", "created_at", "id"),
     )
     __pydantic_model__ = PydanticMessage
 
@@ -78,6 +79,11 @@ class Message(SqlalchemyBase, OrganizationMixin, UserMixin, AgentMixin):
         nullable=True,
         doc="The id of the sender of the message, can be an identity id or agent id",
     )
+    message_type: Mapped[Optional[str]] = mapped_column(
+        nullable=True,
+        default="original",
+        doc="Type of message: 'original' for user input, 'summary' for summarized retained context",
+    )
 
     # Relationships
     agent: Mapped["Agent"] = relationship("Agent", back_populates="messages", lazy="selectin")
diff --git a/mirix/orm/procedural_memory.py b/mirix/orm/procedural_memory.py
index efbbe7a01..db45ad4d2 100755
--- a/mirix/orm/procedural_memory.py
+++ b/mirix/orm/procedural_memory.py
@@ -163,3 +163,27 @@ def user(cls) -> Mapped["User"]:
         Relationship to the User that owns this procedural memory item.
         """
         return relationship("User", lazy="selectin")
+
+    def to_pydantic(self) -> "PydanticProceduralMemoryItem":
+        """
+        Convert to Pydantic model, safely handling relationship loading.
+        This prevents MissingGreenlet errors when converting detached instances.
+        """
+        state = {
+            "id": self.id,
+            "agent_id": self.agent_id,
+            "client_id": self.client_id,
+            "user_id": self.user_id,
+            "organization_id": self.organization_id,
+            "entry_type": self.entry_type,
+            "summary": self.summary,
+            "steps": self.steps,
+            "filter_tags": self.filter_tags,
+            "last_modify": self.last_modify,
+            "embedding_config": self.embedding_config,
+            "summary_embedding": self.summary_embedding,
+            "steps_embedding": self.steps_embedding,
+            "created_at": self.created_at,
+            "updated_at": self.updated_at,
+        }
+        return self.__pydantic_model__(**state)
diff --git a/mirix/orm/resource_memory.py b/mirix/orm/resource_memory.py
index 175e915d7..6b51397e2 100755
--- a/mirix/orm/resource_memory.py
+++ b/mirix/orm/resource_memory.py
@@ -163,3 +163,27 @@ def user(cls) -> Mapped["User"]:
         Relationship to the User that owns this resource memory item.
         """
         return relationship("User", lazy="selectin")
+
+    def to_pydantic(self) -> "PydanticResourceMemoryItem":
+        """
+        Convert to Pydantic model, safely handling relationship loading.
+        This prevents MissingGreenlet errors when converting detached instances.
+        """
+        state = {
+            "id": self.id,
+            "agent_id": self.agent_id,
+            "client_id": self.client_id,
+            "user_id": self.user_id,
+            "organization_id": self.organization_id,
+            "title": self.title,
+            "summary": self.summary,
+            "content": self.content,
+            "resource_type": self.resource_type,
+            "filter_tags": self.filter_tags,
+            "last_modify": self.last_modify,
+            "embedding_config": self.embedding_config,
+            "summary_embedding": self.summary_embedding,
+            "created_at": self.created_at,
+            "updated_at": self.updated_at,
+        }
+        return self.__pydantic_model__(**state)
diff --git a/mirix/orm/semantic_memory.py b/mirix/orm/semantic_memory.py
index 1ee83d578..336cf8730 100755
--- a/mirix/orm/semantic_memory.py
+++ b/mirix/orm/semantic_memory.py
@@ -181,3 +181,29 @@ def user(cls) -> Mapped["User"]:
         Relationship to the User that owns this semantic memory item.
         """
         return relationship("User", lazy="selectin")
+
+    def to_pydantic(self) -> PydanticSemanticMemoryItem:
+        """
+        Convert to Pydantic model, safely handling relationship loading.
+        This prevents MissingGreenlet errors when converting detached instances.
+        """
+        state = {
+            "id": self.id,
+            "agent_id": self.agent_id,
+            "client_id": self.client_id,
+            "user_id": self.user_id,
+            "organization_id": self.organization_id,
+            "name": self.name,
+            "summary": self.summary,
+            "details": self.details,
+            "source": self.source,
+            "filter_tags": self.filter_tags,
+            "last_modify": self.last_modify,
+            "embedding_config": self.embedding_config,
+            "name_embedding": self.name_embedding,
+            "summary_embedding": self.summary_embedding,
+            "details_embedding": self.details_embedding,
+            "created_at": self.created_at,
+            "updated_at": self.updated_at,
+        }
+        return self.__pydantic_model__(**state)
diff --git a/mirix/orm/sqlalchemy_base.py b/mirix/orm/sqlalchemy_base.py
index 8811943e7..ef2009c92 100755
--- a/mirix/orm/sqlalchemy_base.py
+++ b/mirix/orm/sqlalchemy_base.py
@@ -29,6 +29,11 @@
 
 logger = get_logger(__name__)
 
+# Diagnostic flag for MissingGreenlet debugging - set via env var
+import os
+
+_TRACE_MISSING_GREENLET = os.getenv("MIRIX_TRACE_MISSING_GREENLET", "false").lower() == "true"
+
 
 def handle_db_timeout(func):
     """Decorator to handle SQLAlchemy TimeoutError (async-aware)."""
@@ -39,9 +44,7 @@ async def wrapper(*args, **kwargs):
             return await func(*args, **kwargs)
         except TimeoutError as e:
             logger.error("Timeout while executing %s: %s", func.__name__, e)
-            raise DatabaseTimeoutError(
-                message=f"Timeout occurred in {func.__name__}.", original_exception=e
-            ) from e
+            raise DatabaseTimeoutError(message=f"Timeout occurred in {func.__name__}.", original_exception=e) from e
 
     return wrapper
 
@@ -615,6 +618,20 @@ def __pydantic_model__(self) -> "BaseModel":
 
     def to_pydantic(self) -> "BaseModel":
         """converts to the basic pydantic model counterpart"""
+        if _TRACE_MISSING_GREENLET:
+            try:
+                return self.__pydantic_model__.model_validate(self)
+            except Exception as e:
+                if "MissingGreenlet" in str(type(e).__name__) or "greenlet" in str(e).lower():
+                    import traceback
+
+                    logger.error(
+                        "MissingGreenlet detected in to_pydantic for %s (id=%s)\n" "Full traceback:\n%s",
+                        self.__class__.__name__,
+                        getattr(self, "id", "no-id"),
+                        traceback.format_exc(),
+                    )
+                raise
         return self.__pydantic_model__.model_validate(self)
 
     def to_record(self) -> "BaseModel":
@@ -792,8 +809,6 @@ async def _update_redis_cache(self, operation: str = "update", actor: Optional["
                 else:
                     data = self.to_pydantic().model_dump(mode="json")
 
-                    if "message_ids" in data and data["message_ids"]:
-                        data["message_ids"] = json.dumps(data["message_ids"])
                     if "llm_config" in data and data["llm_config"]:
                         data["llm_config"] = json.dumps(data["llm_config"])
                     if "embedding_config" in data and data["embedding_config"]:
diff --git a/mirix/queue/kafka_queue.py b/mirix/queue/kafka_queue.py
index 5b1fad374..5865c11c3 100644
--- a/mirix/queue/kafka_queue.py
+++ b/mirix/queue/kafka_queue.py
@@ -53,10 +53,7 @@ def __init__(
         try:
             from aiokafka import AIOKafkaConsumer, AIOKafkaProducer
         except ImportError:
-            raise ImportError(
-                "aiokafka is required for Kafka support. "
-                "Install it with: pip install aiokafka"
-            )
+            raise ImportError("aiokafka is required for Kafka support. " "Install it with: pip install aiokafka")
 
         logger.info(
             "Initializing Kafka queue: servers=%s, topic=%s, group=%s, format=%s, security=%s",
@@ -165,9 +162,7 @@ async def get(self, timeout: Optional[float] = None) -> QueueMessage:
         logger.debug("Polling Kafka topic %s for messages (timeout=%.1fs)", self.topic, effective_timeout)
 
         try:
-            record = await asyncio.wait_for(
-                self.consumer.getone(), timeout=effective_timeout
-            )
+            record = await asyncio.wait_for(self.consumer.getone(), timeout=effective_timeout)
         except asyncio.TimeoutError:
             logger.debug("No message available from Kafka within timeout")
             raise
diff --git a/mirix/queue/manager.py b/mirix/queue/manager.py
index 53e6614a9..5beac6f49 100644
--- a/mirix/queue/manager.py
+++ b/mirix/queue/manager.py
@@ -7,7 +7,6 @@
 user_id-based partitioning for parallel processing.
 """
 
-import logging
 from typing import Any, List, Optional
 
 from mirix.log import get_logger
diff --git a/mirix/queue/memory_queue.py b/mirix/queue/memory_queue.py
index cd333b49d..4d71efbdf 100644
--- a/mirix/queue/memory_queue.py
+++ b/mirix/queue/memory_queue.py
@@ -7,7 +7,7 @@
 
 import asyncio
 import logging
-from typing import Dict, List, Optional
+from typing import Any, Dict, List, Optional
 
 from mirix.queue.message_pb2 import QueueMessage
 from mirix.queue.queue_interface import QueueInterface
@@ -66,9 +66,7 @@ class PartitionedMemoryQueue(QueueInterface):
     def __init__(self, num_partitions: int = 1, round_robin: bool = False):
         self._num_partitions = max(1, num_partitions)
         self._round_robin = round_robin
-        self._partitions: List[asyncio.Queue[QueueMessage]] = [
-            asyncio.Queue() for _ in range(self._num_partitions)
-        ]
+        self._partitions: List[asyncio.Queue[QueueMessage]] = [asyncio.Queue() for _ in range(self._num_partitions)]
 
         self._user_partition_map: Dict[str, int] = {}
         self._next_partition: int = 0
@@ -89,7 +87,7 @@ def num_partitions(self) -> int:
     def round_robin(self) -> bool:
         return self._round_robin
 
-    async def get_partition_stats(self) -> Dict[str, any]:
+    async def get_partition_stats(self) -> Dict[str, Any]:
         """Get statistics about partition distribution."""
         async with self._partition_lock:
             partition_counts = [0] * self._num_partitions
@@ -145,9 +143,7 @@ async def get(self, timeout: Optional[float] = None) -> QueueMessage:
         """Retrieve from partition 0 (for backward compatibility)."""
         return await self.get_from_partition(0, timeout)
 
-    async def get_from_partition(
-        self, partition_id: int, timeout: Optional[float] = None
-    ) -> QueueMessage:
+    async def get_from_partition(self, partition_id: int, timeout: Optional[float] = None) -> QueueMessage:
         """
         Retrieve a message from a specific partition.
 
@@ -160,15 +156,10 @@ async def get_from_partition(
             ValueError: If partition_id is out of range
         """
         if partition_id < 0 or partition_id >= self._num_partitions:
-            raise ValueError(
-                f"Invalid partition_id {partition_id}, "
-                f"must be 0 to {self._num_partitions - 1}"
-            )
+            raise ValueError(f"Invalid partition_id {partition_id}, " f"must be 0 to {self._num_partitions - 1}")
 
         if timeout is not None:
-            message = await asyncio.wait_for(
-                self._partitions[partition_id].get(), timeout=timeout
-            )
+            message = await asyncio.wait_for(self._partitions[partition_id].get(), timeout=timeout)
         else:
             message = await self._partitions[partition_id].get()
 
diff --git a/mirix/queue/message_pb2.py b/mirix/queue/message_pb2.py
index 32cdfd9c3..5c721bc0b 100644
--- a/mirix/queue/message_pb2.py
+++ b/mirix/queue/message_pb2.py
@@ -9,48 +9,46 @@
 from google.protobuf import runtime_version as _runtime_version
 from google.protobuf import symbol_database as _symbol_database
 from google.protobuf.internal import builder as _builder
+
 _runtime_version.ValidateProtobufRuntimeVersion(
-    _runtime_version.Domain.PUBLIC,
-    5,
-    27,
-    2,
-    '',
-    'mirix/queue/message.proto'
+    _runtime_version.Domain.PUBLIC, 5, 27, 2, "", "mirix/queue/message.proto"
 )
 # @@protoc_insertion_point(imports)
 
 _sym_db = _symbol_database.Default()
 
+# Well-known protos must be in the default pool before AddSerializedFile
+# (protobuf 5+); see google/protobuf/timestamp.proto deps in message.proto.
+from google.protobuf import struct_pb2 as _struct_pb2  # noqa: F401
+from google.protobuf import timestamp_pb2 as _timestamp_pb2  # noqa: F401
 
-from google.protobuf import timestamp_pb2 as google_dot_protobuf_dot_timestamp__pb2
-from google.protobuf import struct_pb2 as google_dot_protobuf_dot_struct__pb2
-
-
-DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x19mirix/queue/message.proto\x12\x05mirix\x1a\x1fgoogle/protobuf/timestamp.proto\x1a\x1cgoogle/protobuf/struct.proto\"\xaf\x05\n\x0cQueueMessage\x12\x11\n\tclient_id\x18\x01 \x01(\t\x12\x10\n\x08\x61gent_id\x18\x02 \x01(\t\x12,\n\x0einput_messages\x18\x03 \x03(\x0b\x32\x14.mirix.MessageCreate\x12\x15\n\x08\x63haining\x18\x04 \x01(\x08H\x00\x88\x01\x01\x12\x14\n\x07user_id\x18\x05 \x01(\tH\x01\x88\x01\x01\x12\x14\n\x07verbose\x18\x06 \x01(\x08H\x02\x88\x01\x01\x12,\n\x0b\x66ilter_tags\x18\x07 \x01(\x0b\x32\x17.google.protobuf.Struct\x12\x16\n\tuse_cache\x18\x08 \x01(\x08H\x03\x88\x01\x01\x12\x18\n\x0boccurred_at\x18\t \x01(\tH\x04\x88\x01\x01\x12\x1e\n\x11langfuse_trace_id\x18\n \x01(\tH\x05\x88\x01\x01\x12$\n\x17langfuse_observation_id\x18\x0b \x01(\tH\x06\x88\x01\x01\x12 \n\x13langfuse_session_id\x18\x0c \x01(\tH\x07\x88\x01\x01\x12\x1d\n\x10langfuse_user_id\x18\r \x01(\tH\x08\x88\x01\x01\x12\x32\n\x11\x62lock_filter_tags\x18\x0e \x01(\x0b\x32\x17.google.protobuf.Struct\x12*\n\x1d\x62lock_filter_tags_update_mode\x18\x0f \x01(\tH\t\x88\x01\x01\x42\x0b\n\t_chainingB\n\n\x08_user_idB\n\n\x08_verboseB\x0c\n\n_use_cacheB\x0e\n\x0c_occurred_atB\x14\n\x12_langfuse_trace_idB\x1a\n\x18_langfuse_observation_idB\x16\n\x14_langfuse_session_idB\x13\n\x11_langfuse_user_idB \n\x1e_block_filter_tags_update_mode\"\xcf\x01\n\x04User\x12\n\n\x02id\x18\x01 \x01(\t\x12\x17\n\x0forganization_id\x18\x02 \x01(\t\x12\x0c\n\x04name\x18\x03 \x01(\t\x12\x0e\n\x06status\x18\x04 \x01(\t\x12\x10\n\x08timezone\x18\x05 \x01(\t\x12.\n\ncreated_at\x18\x06 \x01(\x0b\x32\x1a.google.protobuf.Timestamp\x12.\n\nupdated_at\x18\x07 \x01(\x0b\x32\x1a.google.protobuf.Timestamp\x12\x12\n\nis_deleted\x18\x08 \x01(\x08\"\xd9\x02\n\rMessageCreate\x12\'\n\x04role\x18\x01 \x01(\x0e\x32\x19.mirix.MessageCreate.Role\x12\x16\n\x0ctext_content\x18\x02 \x01(\tH\x00\x12\x37\n\x12structured_content\x18\x03 \x01(\x0b\x32\x19.mirix.MessageContentListH\x00\x12\x11\n\x04name\x18\x04 \x01(\tH\x01\x88\x01\x01\x12\x11\n\x04otid\x18\x05 \x01(\tH\x02\x88\x01\x01\x12\x16\n\tsender_id\x18\x06 \x01(\tH\x03\x88\x01\x01\x12\x15\n\x08group_id\x18\x07 \x01(\tH\x04\x88\x01\x01\"<\n\x04Role\x12\x14\n\x10ROLE_UNSPECIFIED\x10\x00\x12\r\n\tROLE_USER\x10\x01\x12\x0f\n\x0bROLE_SYSTEM\x10\x02\x42\x0e\n\x0c\x63ontent_typeB\x07\n\x05_nameB\x07\n\x05_otidB\x0c\n\n_sender_idB\x0b\n\t_group_id\">\n\x12MessageContentList\x12(\n\x05parts\x18\x01 \x03(\x0b\x32\x19.mirix.MessageContentPart\"\xbc\x01\n\x12MessageContentPart\x12\"\n\x04text\x18\x01 \x01(\x0b\x32\x12.mirix.TextContentH\x00\x12$\n\x05image\x18\x02 \x01(\x0b\x32\x13.mirix.ImageContentH\x00\x12\"\n\x04\x66ile\x18\x03 \x01(\x0b\x32\x12.mirix.FileContentH\x00\x12-\n\ncloud_file\x18\x04 \x01(\x0b\x32\x17.mirix.CloudFileContentH\x00\x42\t\n\x07\x63ontent\"\x1b\n\x0bTextContent\x12\x0c\n\x04text\x18\x01 \x01(\t\"@\n\x0cImageContent\x12\x10\n\x08image_id\x18\x01 \x01(\t\x12\x13\n\x06\x64\x65tail\x18\x02 \x01(\tH\x00\x88\x01\x01\x42\t\n\x07_detail\"\x1e\n\x0b\x46ileContent\x12\x0f\n\x07\x66ile_id\x18\x01 \x01(\t\"*\n\x10\x43loudFileContent\x12\x16\n\x0e\x63loud_file_uri\x18\x01 \x01(\tb\x06proto3')
+DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(
+    b'\n\x19mirix/queue/message.proto\x12\x05mirix\x1a\x1fgoogle/protobuf/timestamp.proto\x1a\x1cgoogle/protobuf/struct.proto"\xaf\x05\n\x0cQueueMessage\x12\x11\n\tclient_id\x18\x01 \x01(\t\x12\x10\n\x08\x61gent_id\x18\x02 \x01(\t\x12,\n\x0einput_messages\x18\x03 \x03(\x0b\x32\x14.mirix.MessageCreate\x12\x15\n\x08\x63haining\x18\x04 \x01(\x08H\x00\x88\x01\x01\x12\x14\n\x07user_id\x18\x05 \x01(\tH\x01\x88\x01\x01\x12\x14\n\x07verbose\x18\x06 \x01(\x08H\x02\x88\x01\x01\x12,\n\x0b\x66ilter_tags\x18\x07 \x01(\x0b\x32\x17.google.protobuf.Struct\x12\x16\n\tuse_cache\x18\x08 \x01(\x08H\x03\x88\x01\x01\x12\x18\n\x0boccurred_at\x18\t \x01(\tH\x04\x88\x01\x01\x12\x1e\n\x11langfuse_trace_id\x18\n \x01(\tH\x05\x88\x01\x01\x12$\n\x17langfuse_observation_id\x18\x0b \x01(\tH\x06\x88\x01\x01\x12 \n\x13langfuse_session_id\x18\x0c \x01(\tH\x07\x88\x01\x01\x12\x1d\n\x10langfuse_user_id\x18\r \x01(\tH\x08\x88\x01\x01\x12\x32\n\x11\x62lock_filter_tags\x18\x0e \x01(\x0b\x32\x17.google.protobuf.Struct\x12*\n\x1d\x62lock_filter_tags_update_mode\x18\x0f \x01(\tH\t\x88\x01\x01\x42\x0b\n\t_chainingB\n\n\x08_user_idB\n\n\x08_verboseB\x0c\n\n_use_cacheB\x0e\n\x0c_occurred_atB\x14\n\x12_langfuse_trace_idB\x1a\n\x18_langfuse_observation_idB\x16\n\x14_langfuse_session_idB\x13\n\x11_langfuse_user_idB \n\x1e_block_filter_tags_update_mode"\xcf\x01\n\x04User\x12\n\n\x02id\x18\x01 \x01(\t\x12\x17\n\x0forganization_id\x18\x02 \x01(\t\x12\x0c\n\x04name\x18\x03 \x01(\t\x12\x0e\n\x06status\x18\x04 \x01(\t\x12\x10\n\x08timezone\x18\x05 \x01(\t\x12.\n\ncreated_at\x18\x06 \x01(\x0b\x32\x1a.google.protobuf.Timestamp\x12.\n\nupdated_at\x18\x07 \x01(\x0b\x32\x1a.google.protobuf.Timestamp\x12\x12\n\nis_deleted\x18\x08 \x01(\x08"\xd9\x02\n\rMessageCreate\x12\'\n\x04role\x18\x01 \x01(\x0e\x32\x19.mirix.MessageCreate.Role\x12\x16\n\x0ctext_content\x18\x02 \x01(\tH\x00\x12\x37\n\x12structured_content\x18\x03 \x01(\x0b\x32\x19.mirix.MessageContentListH\x00\x12\x11\n\x04name\x18\x04 \x01(\tH\x01\x88\x01\x01\x12\x11\n\x04otid\x18\x05 \x01(\tH\x02\x88\x01\x01\x12\x16\n\tsender_id\x18\x06 \x01(\tH\x03\x88\x01\x01\x12\x15\n\x08group_id\x18\x07 \x01(\tH\x04\x88\x01\x01"<\n\x04Role\x12\x14\n\x10ROLE_UNSPECIFIED\x10\x00\x12\r\n\tROLE_USER\x10\x01\x12\x0f\n\x0bROLE_SYSTEM\x10\x02\x42\x0e\n\x0c\x63ontent_typeB\x07\n\x05_nameB\x07\n\x05_otidB\x0c\n\n_sender_idB\x0b\n\t_group_id">\n\x12MessageContentList\x12(\n\x05parts\x18\x01 \x03(\x0b\x32\x19.mirix.MessageContentPart"\xbc\x01\n\x12MessageContentPart\x12"\n\x04text\x18\x01 \x01(\x0b\x32\x12.mirix.TextContentH\x00\x12$\n\x05image\x18\x02 \x01(\x0b\x32\x13.mirix.ImageContentH\x00\x12"\n\x04\x66ile\x18\x03 \x01(\x0b\x32\x12.mirix.FileContentH\x00\x12-\n\ncloud_file\x18\x04 \x01(\x0b\x32\x17.mirix.CloudFileContentH\x00\x42\t\n\x07\x63ontent"\x1b\n\x0bTextContent\x12\x0c\n\x04text\x18\x01 \x01(\t"@\n\x0cImageContent\x12\x10\n\x08image_id\x18\x01 \x01(\t\x12\x13\n\x06\x64\x65tail\x18\x02 \x01(\tH\x00\x88\x01\x01\x42\t\n\x07_detail"\x1e\n\x0b\x46ileContent\x12\x0f\n\x07\x66ile_id\x18\x01 \x01(\t"*\n\x10\x43loudFileContent\x12\x16\n\x0e\x63loud_file_uri\x18\x01 \x01(\tb\x06proto3'
+)
 
 _globals = globals()
 _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals)
-_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'mirix.queue.message_pb2', _globals)
+_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, "mirix.queue.message_pb2", _globals)
 if not _descriptor._USE_C_DESCRIPTORS:
-  DESCRIPTOR._loaded_options = None
-  _globals['_QUEUEMESSAGE']._serialized_start=100
-  _globals['_QUEUEMESSAGE']._serialized_end=787
-  _globals['_USER']._serialized_start=790
-  _globals['_USER']._serialized_end=997
-  _globals['_MESSAGECREATE']._serialized_start=1000
-  _globals['_MESSAGECREATE']._serialized_end=1345
-  _globals['_MESSAGECREATE_ROLE']._serialized_start=1224
-  _globals['_MESSAGECREATE_ROLE']._serialized_end=1284
-  _globals['_MESSAGECONTENTLIST']._serialized_start=1347
-  _globals['_MESSAGECONTENTLIST']._serialized_end=1409
-  _globals['_MESSAGECONTENTPART']._serialized_start=1412
-  _globals['_MESSAGECONTENTPART']._serialized_end=1600
-  _globals['_TEXTCONTENT']._serialized_start=1602
-  _globals['_TEXTCONTENT']._serialized_end=1629
-  _globals['_IMAGECONTENT']._serialized_start=1631
-  _globals['_IMAGECONTENT']._serialized_end=1695
-  _globals['_FILECONTENT']._serialized_start=1697
-  _globals['_FILECONTENT']._serialized_end=1727
-  _globals['_CLOUDFILECONTENT']._serialized_start=1729
-  _globals['_CLOUDFILECONTENT']._serialized_end=1771
+    DESCRIPTOR._loaded_options = None
+    _globals["_QUEUEMESSAGE"]._serialized_start = 100
+    _globals["_QUEUEMESSAGE"]._serialized_end = 787
+    _globals["_USER"]._serialized_start = 790
+    _globals["_USER"]._serialized_end = 997
+    _globals["_MESSAGECREATE"]._serialized_start = 1000
+    _globals["_MESSAGECREATE"]._serialized_end = 1345
+    _globals["_MESSAGECREATE_ROLE"]._serialized_start = 1224
+    _globals["_MESSAGECREATE_ROLE"]._serialized_end = 1284
+    _globals["_MESSAGECONTENTLIST"]._serialized_start = 1347
+    _globals["_MESSAGECONTENTLIST"]._serialized_end = 1409
+    _globals["_MESSAGECONTENTPART"]._serialized_start = 1412
+    _globals["_MESSAGECONTENTPART"]._serialized_end = 1600
+    _globals["_TEXTCONTENT"]._serialized_start = 1602
+    _globals["_TEXTCONTENT"]._serialized_end = 1629
+    _globals["_IMAGECONTENT"]._serialized_start = 1631
+    _globals["_IMAGECONTENT"]._serialized_end = 1695
+    _globals["_FILECONTENT"]._serialized_start = 1697
+    _globals["_FILECONTENT"]._serialized_end = 1727
+    _globals["_CLOUDFILECONTENT"]._serialized_start = 1729
+    _globals["_CLOUDFILECONTENT"]._serialized_end = 1771
 # @@protoc_insertion_point(module_scope)
diff --git a/mirix/queue/message_pb2.pyi b/mirix/queue/message_pb2.pyi
index 4822f24f9..854e25c2d 100644
--- a/mirix/queue/message_pb2.pyi
+++ b/mirix/queue/message_pb2.pyi
@@ -1,15 +1,36 @@
-from google.protobuf import timestamp_pb2 as _timestamp_pb2
+from typing import ClassVar as _ClassVar
+from typing import Iterable as _Iterable
+from typing import Mapping as _Mapping
+from typing import Optional as _Optional
+from typing import Union as _Union
+
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import message as _message
 from google.protobuf import struct_pb2 as _struct_pb2
+from google.protobuf import timestamp_pb2 as _timestamp_pb2
 from google.protobuf.internal import containers as _containers
 from google.protobuf.internal import enum_type_wrapper as _enum_type_wrapper
-from google.protobuf import descriptor as _descriptor
-from google.protobuf import message as _message
-from typing import ClassVar as _ClassVar, Iterable as _Iterable, Mapping as _Mapping, Optional as _Optional, Union as _Union
 
 DESCRIPTOR: _descriptor.FileDescriptor
 
 class QueueMessage(_message.Message):
-    __slots__ = ("client_id", "agent_id", "input_messages", "chaining", "user_id", "verbose", "filter_tags", "use_cache", "occurred_at", "langfuse_trace_id", "langfuse_observation_id", "langfuse_session_id", "langfuse_user_id", "block_filter_tags", "block_filter_tags_update_mode")
+    __slots__ = (
+        "client_id",
+        "agent_id",
+        "input_messages",
+        "chaining",
+        "user_id",
+        "verbose",
+        "filter_tags",
+        "use_cache",
+        "occurred_at",
+        "langfuse_trace_id",
+        "langfuse_observation_id",
+        "langfuse_session_id",
+        "langfuse_user_id",
+        "block_filter_tags",
+        "block_filter_tags_update_mode",
+    )
     CLIENT_ID_FIELD_NUMBER: _ClassVar[int]
     AGENT_ID_FIELD_NUMBER: _ClassVar[int]
     INPUT_MESSAGES_FIELD_NUMBER: _ClassVar[int]
@@ -40,7 +61,24 @@ class QueueMessage(_message.Message):
     langfuse_user_id: str
     block_filter_tags: _struct_pb2.Struct
     block_filter_tags_update_mode: str
-    def __init__(self, client_id: _Optional[str] = ..., agent_id: _Optional[str] = ..., input_messages: _Optional[_Iterable[_Union[MessageCreate, _Mapping]]] = ..., chaining: bool = ..., user_id: _Optional[str] = ..., verbose: bool = ..., filter_tags: _Optional[_Union[_struct_pb2.Struct, _Mapping]] = ..., use_cache: bool = ..., occurred_at: _Optional[str] = ..., langfuse_trace_id: _Optional[str] = ..., langfuse_observation_id: _Optional[str] = ..., langfuse_session_id: _Optional[str] = ..., langfuse_user_id: _Optional[str] = ..., block_filter_tags: _Optional[_Union[_struct_pb2.Struct, _Mapping]] = ..., block_filter_tags_update_mode: _Optional[str] = ...) -> None: ...
+    def __init__(
+        self,
+        client_id: _Optional[str] = ...,
+        agent_id: _Optional[str] = ...,
+        input_messages: _Optional[_Iterable[_Union[MessageCreate, _Mapping]]] = ...,
+        chaining: bool = ...,
+        user_id: _Optional[str] = ...,
+        verbose: bool = ...,
+        filter_tags: _Optional[_Union[_struct_pb2.Struct, _Mapping]] = ...,
+        use_cache: bool = ...,
+        occurred_at: _Optional[str] = ...,
+        langfuse_trace_id: _Optional[str] = ...,
+        langfuse_observation_id: _Optional[str] = ...,
+        langfuse_session_id: _Optional[str] = ...,
+        langfuse_user_id: _Optional[str] = ...,
+        block_filter_tags: _Optional[_Union[_struct_pb2.Struct, _Mapping]] = ...,
+        block_filter_tags_update_mode: _Optional[str] = ...,
+    ) -> None: ...
 
 class User(_message.Message):
     __slots__ = ("id", "organization_id", "name", "status", "timezone", "created_at", "updated_at", "is_deleted")
@@ -60,15 +98,27 @@ class User(_message.Message):
     created_at: _timestamp_pb2.Timestamp
     updated_at: _timestamp_pb2.Timestamp
     is_deleted: bool
-    def __init__(self, id: _Optional[str] = ..., organization_id: _Optional[str] = ..., name: _Optional[str] = ..., status: _Optional[str] = ..., timezone: _Optional[str] = ..., created_at: _Optional[_Union[_timestamp_pb2.Timestamp, _Mapping]] = ..., updated_at: _Optional[_Union[_timestamp_pb2.Timestamp, _Mapping]] = ..., is_deleted: bool = ...) -> None: ...
+    def __init__(
+        self,
+        id: _Optional[str] = ...,
+        organization_id: _Optional[str] = ...,
+        name: _Optional[str] = ...,
+        status: _Optional[str] = ...,
+        timezone: _Optional[str] = ...,
+        created_at: _Optional[_Union[_timestamp_pb2.Timestamp, _Mapping]] = ...,
+        updated_at: _Optional[_Union[_timestamp_pb2.Timestamp, _Mapping]] = ...,
+        is_deleted: bool = ...,
+    ) -> None: ...
 
 class MessageCreate(_message.Message):
     __slots__ = ("role", "text_content", "structured_content", "name", "otid", "sender_id", "group_id")
+
     class Role(int, metaclass=_enum_type_wrapper.EnumTypeWrapper):
         __slots__ = ()
         ROLE_UNSPECIFIED: _ClassVar[MessageCreate.Role]
         ROLE_USER: _ClassVar[MessageCreate.Role]
         ROLE_SYSTEM: _ClassVar[MessageCreate.Role]
+
     ROLE_UNSPECIFIED: MessageCreate.Role
     ROLE_USER: MessageCreate.Role
     ROLE_SYSTEM: MessageCreate.Role
@@ -86,7 +136,16 @@ class MessageCreate(_message.Message):
     otid: str
     sender_id: str
     group_id: str
-    def __init__(self, role: _Optional[_Union[MessageCreate.Role, str]] = ..., text_content: _Optional[str] = ..., structured_content: _Optional[_Union[MessageContentList, _Mapping]] = ..., name: _Optional[str] = ..., otid: _Optional[str] = ..., sender_id: _Optional[str] = ..., group_id: _Optional[str] = ...) -> None: ...
+    def __init__(
+        self,
+        role: _Optional[_Union[MessageCreate.Role, str]] = ...,
+        text_content: _Optional[str] = ...,
+        structured_content: _Optional[_Union[MessageContentList, _Mapping]] = ...,
+        name: _Optional[str] = ...,
+        otid: _Optional[str] = ...,
+        sender_id: _Optional[str] = ...,
+        group_id: _Optional[str] = ...,
+    ) -> None: ...
 
 class MessageContentList(_message.Message):
     __slots__ = ("parts",)
@@ -104,7 +163,13 @@ class MessageContentPart(_message.Message):
     image: ImageContent
     file: FileContent
     cloud_file: CloudFileContent
-    def __init__(self, text: _Optional[_Union[TextContent, _Mapping]] = ..., image: _Optional[_Union[ImageContent, _Mapping]] = ..., file: _Optional[_Union[FileContent, _Mapping]] = ..., cloud_file: _Optional[_Union[CloudFileContent, _Mapping]] = ...) -> None: ...
+    def __init__(
+        self,
+        text: _Optional[_Union[TextContent, _Mapping]] = ...,
+        image: _Optional[_Union[ImageContent, _Mapping]] = ...,
+        file: _Optional[_Union[FileContent, _Mapping]] = ...,
+        cloud_file: _Optional[_Union[CloudFileContent, _Mapping]] = ...,
+    ) -> None: ...
 
 class TextContent(_message.Message):
     __slots__ = ("text",)
diff --git a/mirix/queue/message_pb2_grpc.py b/mirix/queue/message_pb2_grpc.py
index e4a393dc2..ae29b37a4 100644
--- a/mirix/queue/message_pb2_grpc.py
+++ b/mirix/queue/message_pb2_grpc.py
@@ -1,24 +1,24 @@
 # Generated by the gRPC Python protocol compiler plugin. DO NOT EDIT!
 """Client and server classes corresponding to protobuf-defined services."""
-import grpc
-import warnings
 
+import grpc
 
-GRPC_GENERATED_VERSION = '1.66.2'
+GRPC_GENERATED_VERSION = "1.66.2"
 GRPC_VERSION = grpc.__version__
 _version_not_supported = False
 
 try:
     from grpc._utilities import first_version_is_lower
+
     _version_not_supported = first_version_is_lower(GRPC_VERSION, GRPC_GENERATED_VERSION)
 except ImportError:
     _version_not_supported = True
 
 if _version_not_supported:
     raise RuntimeError(
-        f'The grpc package installed is at version {GRPC_VERSION},'
-        + f' but the generated code in mirix/queue/message_pb2_grpc.py depends on'
-        + f' grpcio>={GRPC_GENERATED_VERSION}.'
-        + f' Please upgrade your grpc module to grpcio>={GRPC_GENERATED_VERSION}'
-        + f' or downgrade your generated code using grpcio-tools<={GRPC_VERSION}.'
+        f"The grpc package installed is at version {GRPC_VERSION},"
+        + " but the generated code in mirix/queue/message_pb2_grpc.py depends on"
+        + f" grpcio>={GRPC_GENERATED_VERSION}."
+        + f" Please upgrade your grpc module to grpcio>={GRPC_GENERATED_VERSION}"
+        + f" or downgrade your generated code using grpcio-tools<={GRPC_VERSION}."
     )
diff --git a/mirix/queue/queue_util.py b/mirix/queue/queue_util.py
index deea94891..892a5a97a 100644
--- a/mirix/queue/queue_util.py
+++ b/mirix/queue/queue_util.py
@@ -8,11 +8,9 @@
 from mirix.observability import add_trace_to_queue_message
 from mirix.queue.message_pb2 import MessageCreate as ProtoMessageCreate
 from mirix.queue.message_pb2 import QueueMessage
-from mirix.queue.message_pb2 import User as ProtoUser
 from mirix.schemas.client import Client
 from mirix.schemas.enums import MessageRole
 from mirix.schemas.message import MessageCreate
-from mirix.schemas.message import MessageCreate as PydanticMessageCreate
 from mirix.schemas.mirix_message_content import TextContent
 
 logger = logging.getLogger(__name__)
diff --git a/mirix/queue/worker.py b/mirix/queue/worker.py
index 2cde1df6a..59fe0c850 100644
--- a/mirix/queue/worker.py
+++ b/mirix/queue/worker.py
@@ -18,7 +18,6 @@
 if TYPE_CHECKING:
     from mirix.schemas.client import Client
     from mirix.schemas.message import MessageCreate
-    from mirix.schemas.user import User
 
     from .queue_interface import QueueInterface
 
@@ -154,9 +153,7 @@ async def _process_message_async(self, message: QueueMessage) -> None:
             async def _resolve_actor_and_user():
                 actor = await server.client_manager.get_client_by_id(client_id)
                 if not actor:
-                    raise ValueError(
-                        f"Client with id={client_id} not found in database"
-                    )
+                    raise ValueError(f"Client with id={client_id} not found in database")
 
                 user_manager = UserManager()
                 if user_id:
@@ -189,8 +186,7 @@ async def _resolve_actor_and_user():
                             )
                         except Exception as create_error:
                             logger.error(
-                                "Failed to auto-create user with id=%s: %s. "
-                                "Falling back to admin user.",
+                                "Failed to auto-create user with id=%s: %s. " "Falling back to admin user.",
                                 user_id,
                                 create_error,
                             )
@@ -218,9 +214,7 @@ async def _resolve_actor_and_user():
                     raise ValueError("block_filter_tags was provided but could not be parsed as a dict") from e
 
             block_filter_tags_update_mode = (
-                message.block_filter_tags_update_mode
-                if message.HasField("block_filter_tags_update_mode")
-                else "merge"
+                message.block_filter_tags_update_mode if message.HasField("block_filter_tags_update_mode") else "merge"
             )
 
             # Log the processing
@@ -306,9 +300,7 @@ async def _consume_loop(self) -> None:
         while self._running:
             try:
                 if self._partition_id is not None and hasattr(self.queue, "get_from_partition"):
-                    message = await self.queue.get_from_partition(
-                        self._partition_id, timeout=1.0
-                    )
+                    message = await self.queue.get_from_partition(self._partition_id, timeout=1.0)
                 else:
                     message = await self.queue.get(timeout=1.0)
 
diff --git a/mirix/schemas/agent.py b/mirix/schemas/agent.py
index 59930ec59..6bc304e1a 100755
--- a/mirix/schemas/agent.py
+++ b/mirix/schemas/agent.py
@@ -8,7 +8,7 @@
 from mirix.schemas.block import CreateBlock
 from mirix.schemas.embedding_config import EmbeddingConfig
 from mirix.schemas.llm_config import LLMConfig
-from mirix.schemas.message import Message, MessageCreate
+from mirix.schemas.message import Message
 from mirix.schemas.mirix_base import OrmMetadataBase
 from mirix.schemas.openai.chat_completion_response import UsageStatistics
 from mirix.schemas.tool import Tool
@@ -23,7 +23,7 @@ class AgentType(str, Enum):
     """
 
     coder_agent = "coder_agent"
-    chat_agent = "chat_agent"
+    chat_agent = "chat_agent"  # DEPRECATED: use a memory agent type instead
     reflexion_agent = "reflexion_agent"
     background_agent = "background_agent"
     episodic_memory_agent = "episodic_memory_agent"
@@ -58,12 +58,6 @@ class AgentState(OrmMetadataBase, validate_assignment=True):
     # tool rules
     tool_rules: Optional[List[ToolRule]] = Field(default=None, description="The list of tool rules.")
 
-    # in-context memory
-    message_ids: Optional[List[str]] = Field(
-        default=None,
-        description="The ids of the messages in the agent's in-context memory.",
-    )
-
     # system prompt
     system: str = Field(..., description="The system prompt used by the agent.")
 
@@ -135,12 +129,6 @@ class CreateAgent(BaseModel, validate_assignment=True):  #
     embedding_config: Optional[EmbeddingConfig] = Field(
         None, description="The embedding configuration used by the agent."
     )
-    # Note: if this is None, then we'll populate with the standard "more human than human" initial message sequence
-    # If the client wants to make this empty, then the client can set the arg to an empty list
-    initial_message_sequence: Optional[List[MessageCreate]] = Field(
-        None,
-        description="The initial set of messages to put in the agent's in-context memory.",
-    )
     include_base_tools: bool = Field(
         True,
         description="If true, attaches the Mirix core tools (e.g. archival_memory and core_memory related functions).",
@@ -236,9 +224,6 @@ class UpdateAgent(BaseModel):
     embedding_config: Optional[EmbeddingConfig] = Field(
         None, description="The embedding configuration used by the agent."
     )
-    message_ids: Optional[List[str]] = Field(
-        None, description="The ids of the messages in the agent's in-context memory."
-    )
     description: Optional[str] = Field(None, description="The description of the agent.")
     parent_id: Optional[str] = Field(None, description="The parent agent ID (for sub-agents in a meta-agent).")
     mcp_tools: Optional[List[str]] = Field(None, description="List of MCP server names to connect to this agent.")
@@ -317,10 +302,6 @@ class AgentStepResponse(BaseModel):
         description="Whether the agent requested a contine_chaining (i.e. follow-up execution).",
     )
     function_failed: bool = Field(..., description="Whether the agent step ended because a function call failed.")
-    in_context_memory_warning: bool = Field(
-        ...,
-        description="Whether the agent step ended because the in-context memory is near its limit.",
-    )
     usage: UsageStatistics = Field(..., description="Usage statistics of the LLM call during the agent's step.")
     traj: Optional[dict] = Field(None, description="Action, Observation, State at the current step")
 
diff --git a/mirix/schemas/client.py b/mirix/schemas/client.py
index ccac0d2f9..d4d46f435 100644
--- a/mirix/schemas/client.py
+++ b/mirix/schemas/client.py
@@ -46,6 +46,11 @@ class Client(ClientBase):
     write_scope: Optional[str] = Field(default=None, description="Scope for writing memories (null = read-only).")
     read_scopes: List[str] = Field(default_factory=list, description="Scopes for reading memories.")
 
+    # Message retention
+    message_set_retention_count: Optional[int] = Field(
+        default=0, description="Number of input message-sets to retain per (agent, user). 0 = no retention."
+    )
+
     # Dashboard authentication fields
     email: Optional[str] = Field(default=None, description="Email address for dashboard login.")
     password_hash: Optional[str] = Field(default=None, description="Hashed password for dashboard login.")
@@ -72,3 +77,6 @@ class ClientUpdate(ClientBase):
     write_scope: Optional[str] = Field(default=None, description="The new write scope of the client.")
     read_scopes: Optional[List[str]] = Field(default=None, description="The new read scopes of the client.")
     organization_id: Optional[str] = Field(default=None, description="The new organization id of the client.")
+    message_set_retention_count: Optional[int] = Field(
+        default=None, description="Number of input message-sets to retain per (agent, user). 0 = no retention."
+    )
diff --git a/mirix/schemas/memory.py b/mirix/schemas/memory.py
index e00f4b99b..30cd07b73 100755
--- a/mirix/schemas/memory.py
+++ b/mirix/schemas/memory.py
@@ -5,59 +5,13 @@
 
 # Forward referencing to avoid circular import with Agent -> Memory -> Agent
 if TYPE_CHECKING:
-    from mirix.schemas.agent import AgentState
+    pass
 
 from mirix.constants import CORE_MEMORY_BLOCK_CHAR_LIMIT
 from mirix.schemas.block import Block
-from mirix.schemas.message import Message
-from mirix.schemas.openai.chat_completion_request import Tool
 from mirix.schemas.user import User as PydanticUser
 
 
-class ContextWindowOverview(BaseModel):
-    """
-    Overview of the context window, including the number of messages and tokens.
-    """
-
-    # top-level information
-    context_window_size_max: int = Field(..., description="The maximum amount of tokens the context window can hold.")
-    context_window_size_current: int = Field(..., description="The current number of tokens in the context window.")
-
-    # context window breakdown (in messages)
-    # (technically not in the context window, but useful to know)
-    num_messages: int = Field(..., description="The number of messages in the context window.")
-    num_archival_memory: int = Field(..., description="The number of messages in the archival memory.")
-    num_recall_memory: int = Field(..., description="The number of messages in the recall memory.")
-    num_tokens_external_memory_summary: int = Field(
-        ...,
-        description="The number of tokens in the external memory summary (archival + recall metadata).",
-    )
-    external_memory_summary: str = Field(
-        ...,
-        description="The metadata summary of the external memory sources (archival + recall metadata).",
-    )
-
-    # context window breakdown (in tokens)
-    # this should all add up to context_window_size_current
-
-    num_tokens_system: int = Field(..., description="The number of tokens in the system prompt.")
-    system_prompt: str = Field(..., description="The content of the system prompt.")
-
-    num_tokens_core_memory: int = Field(..., description="The number of tokens in the core memory.")
-    core_memory: str = Field(..., description="The content of the core memory.")
-
-    num_tokens_summary_memory: int = Field(..., description="The number of tokens in the summary memory.")
-    summary_memory: Optional[str] = Field(None, description="The content of the summary memory.")
-
-    num_tokens_functions_definitions: int = Field(..., description="The number of tokens in the functions definitions.")
-    functions_definitions: Optional[List[Tool]] = Field(..., description="The content of the functions definitions.")
-
-    num_tokens_messages: int = Field(..., description="The number of tokens in the messages list.")
-    # TODO make list of messages?
-    # messages: List[dict] = Field(..., description="The messages in the context window.")
-    messages: List[Message] = Field(..., description="The messages in the context window.")
-
-
 def line_numbers(value: str, prefix: str = "Line ") -> str:
     """
     Turn
diff --git a/mirix/schemas/message.py b/mirix/schemas/message.py
index d3ece01cc..bd616fbf4 100644
--- a/mirix/schemas/message.py
+++ b/mirix/schemas/message.py
@@ -1,10 +1,8 @@
 from __future__ import annotations
 
-import copy
 import json
 import uuid
 import warnings
-from collections import OrderedDict
 from datetime import datetime, timezone
 from typing import Any, Dict, List, Literal, Optional, Union
 
@@ -172,6 +170,11 @@ class Message(BaseMessage):
         ],
     )
 
+    message_type: Optional[str] = Field(
+        default="original",
+        description="Type of message: 'original' for user input, 'summary' for summarized retained context",
+    )
+
     @field_validator("role")
     @classmethod
     def validate_role(cls, v: str) -> str:
@@ -609,8 +612,8 @@ def dict_to_message(
             if openai_message_dict["role"] == "assistant":
                 if not content and tool_calls is None:
                     raise ValueError(
-                        f"Invalid assistant message: must have content or tool_calls. "
-                        f"Got empty content and no tool_calls."
+                        "Invalid assistant message: must have content or tool_calls. "
+                        "Got empty content and no tool_calls."
                     )
 
             # If we're going from tool-call style
diff --git a/mirix/schemas/mirix_base.py b/mirix/schemas/mirix_base.py
index 4890489f9..1a1f9f06e 100755
--- a/mirix/schemas/mirix_base.py
+++ b/mirix/schemas/mirix_base.py
@@ -5,6 +5,7 @@
 from uuid import UUID
 
 from pydantic import BaseModel, ConfigDict, Field, field_validator
+from pydantic.fields import FieldInfo
 
 # from: https://gist.github.com/norton120/22242eadb80bf2cf1dd54a961b151c61
 
@@ -30,7 +31,7 @@ class MirixBase(BaseModel):
     #    raise NotImplementedError("All schemas must have an __id_prefix__ attribute!")
 
     @classmethod
-    def generate_id_field(cls, prefix: Optional[str] = None) -> "Field":
+    def generate_id_field(cls, prefix: Optional[str] = None) -> FieldInfo:
         prefix = prefix or cls.__id_prefix__
 
         return Field(
diff --git a/mirix/schemas/openai/chat_completion_request.py b/mirix/schemas/openai/chat_completion_request.py
index 1e5c26d7a..69b2fba69 100755
--- a/mirix/schemas/openai/chat_completion_request.py
+++ b/mirix/schemas/openai/chat_completion_request.py
@@ -70,7 +70,6 @@ class FunctionCall(BaseModel):
 class ToolFunctionChoice(BaseModel):
     # The type of the tool. Currently, only function is supported
     type: Literal["function"] = "function"
-    # type: str = Field(default="function", const=True)
     function: FunctionCall
 
 
@@ -87,7 +86,6 @@ class FunctionSchema(BaseModel):
 class Tool(BaseModel):
     # The type of the tool. Currently, only function is supported
     type: Literal["function"] = "function"
-    # type: str = Field(default="function", const=True)
     function: FunctionSchema
 
 
diff --git a/mirix/schemas/openai/chat_completions.py b/mirix/schemas/openai/chat_completions.py
index da1957771..43c03e359 100755
--- a/mirix/schemas/openai/chat_completions.py
+++ b/mirix/schemas/openai/chat_completions.py
@@ -70,7 +70,6 @@ class FunctionCall(BaseModel):
 class ToolFunctionChoice(BaseModel):
     # The type of the tool. Currently, only function is supported
     type: Literal["function"] = "function"
-    # type: str = Field(default="function", const=True)
     function: FunctionCall
 
 
@@ -87,7 +86,6 @@ class FunctionSchema(BaseModel):
 class Tool(BaseModel):
     # The type of the tool. Currently, only function is supported
     type: Literal["function"] = "function"
-    # type: str = Field(default="function", const=True)
     function: FunctionSchema
 
 
diff --git a/mirix/schemas/providers.py b/mirix/schemas/providers.py
index a3e5c7b4e..011ceff2f 100755
--- a/mirix/schemas/providers.py
+++ b/mirix/schemas/providers.py
@@ -5,7 +5,6 @@
 from pydantic import Field, model_validator
 
 from mirix.constants import LLM_MAX_TOKENS, MIN_CONTEXT_WINDOW
-from mirix.utils import smart_urljoin
 from mirix.llm_api.azure_openai import (
     get_azure_chat_completions_endpoint,
     get_azure_embeddings_endpoint,
@@ -15,6 +14,7 @@
 from mirix.schemas.embedding_config import EmbeddingConfig
 from mirix.schemas.llm_config import LLMConfig
 from mirix.schemas.mirix_base import MirixBase
+from mirix.utils import smart_urljoin
 
 logger = get_logger(__name__)
 
diff --git a/mirix/sdk.py b/mirix/sdk.py
index 8632c4ae4..ab8b2570c 100644
--- a/mirix/sdk.py
+++ b/mirix/sdk.py
@@ -4,7 +4,6 @@
 All I/O methods are async. Use Mirix.create() to construct an instance.
 """
 
-import asyncio
 import logging
 import os
 from pathlib import Path
@@ -133,6 +132,7 @@ async def create(
             os.environ[f"{model_provider.upper()}_API_KEY"] = api_key
         import mirix.settings
         from mirix.settings import ModelSettings
+
         new_settings = ModelSettings()
         for field_name in ModelSettings.model_fields:
             setattr(
@@ -148,6 +148,7 @@ async def create(
             config_path = Path(config_path)
             if config_path.exists():
                 import yaml
+
                 with open(config_path, "r") as f:
                     config_data = yaml.safe_load(f)
                     system_prompts_folder = config_data.get("system_prompts_folder")
@@ -211,9 +212,7 @@ async def add(self, content: str, **kwargs) -> Dict[str, Any]:
             await memory_agent.add("John likes pizza")
         """
         self._require_meta_agent()
-        response = await self._client.send_message(
-            agent_id=self._meta_agent.id, role="user", message=content, **kwargs
-        )
+        response = await self._client.send_message(agent_id=self._meta_agent.id, role="user", message=content, **kwargs)
         if hasattr(response, "messages") and response.messages:
             for msg in reversed(response.messages):
                 if msg.role == "assistant":
@@ -246,44 +245,17 @@ async def get_user_by_name(self, user_name: str):
                 return user
         return None
 
-    def clear(self) -> Dict[str, Any]:
-        """
-        Clear all memories.
-
-        Note: This requires manual database file removal and app restart.
-
-        Returns:
-            Dict with warning message and instructions
-
-        Example:
-            result = memory_agent.clear()
-            logger.debug(result['warning'])
-            for step in result['instructions']:
-                logger.debug(step)
-        """
-        return {
-            "success": False,
-            "warning": "Memory clearing requires manual database reset.",
-            "instructions": [
-                "1. Stop the Mirix application/process",
-                "2. Remove the database file: ~/.mirix/sqlite.db",
-                "3. Restart the Mirix application",
-                "4. Initialize a new Mirix agent",
-            ],
-            "manual_command": "rm ~/.mirix/sqlite.db",
-            "note": "After removing the database file, you must restart your application and create a new agent instance.",
-        }
-
     async def clear_conversation_history(self, user_id: Optional[str] = None) -> Dict[str, Any]:
         """
         Clear conversation history while preserving memories.
 
-        This removes user and assistant messages from the conversation
-        history but keeps system messages and all stored memories intact.
+        This removes persisted conversation message rows while preserving
+        memory tables and agent configuration.
 
         Args:
-            user_id: User ID to clear messages for. If None, clears all messages
-                    except system messages. If provided, only clears messages for that specific user.
+            user_id: User ID to clear messages for. If None, clears all retained
+                    conversation rows for the meta agent. If provided, only clears
+                    messages for that specific user.
 
         Returns:
             Dict containing success status, message, and count of deleted messages
@@ -303,24 +275,15 @@ async def clear_conversation_history(self, user_id: Optional[str] = None) -> Dic
         self._require_meta_agent()
         try:
             if user_id is None:
-                agent_state = await self._client.server.agent_manager.get_agent_by_id(
-                    agent_id=self._meta_agent.id,
-                    actor=self._client.client,
-                )
-                current_messages = await self._client.server.agent_manager.get_in_context_messages(
-                    agent_state=agent_state,
-                    actor=self._client.client,
-                )
-                messages_count = len(current_messages)
+                messages_count = 0  # count not available without per-user query
                 await self._client.server.agent_manager.reset_messages(
                     agent_id=self._meta_agent.id,
                     actor=self._client.client,
                     user_id=None,
-                    add_default_initial_messages=True,
                 )
                 return {
                     "success": True,
-                    "message": "Successfully cleared conversation history. All user and assistant messages removed (system messages preserved).",
+                    "message": "Successfully cleared retained conversation history.",
                     "messages_deleted": messages_count,
                 }
             else:
@@ -331,76 +294,26 @@ async def clear_conversation_history(self, user_id: Optional[str] = None) -> Dic
                         "error": f"User with ID '{user_id}' not found",
                         "messages_deleted": 0,
                     }
-                agent_state = await self._client.server.agent_manager.get_agent_by_id(
+                current_messages = await self._client.server.message_manager.get_messages_for_agent_user(
                     agent_id=self._meta_agent.id,
+                    user_id=target_user.id,
                     actor=self._client.client,
+                    limit=10000,
                 )
-                current_messages = await self._client.server.agent_manager.get_in_context_messages(
-                    agent_state=agent_state,
-                    actor=self._client.client,
-                    user=target_user,
-                )
-                user_messages_count = len(
-                    [msg for msg in current_messages if msg.role != "system" and msg.user_id == target_user.id]
-                )
+                user_messages_count = len(current_messages)
                 await self._client.server.agent_manager.reset_messages(
                     agent_id=self._meta_agent.id,
                     actor=self._client.client,
                     user_id=target_user.id,
-                    add_default_initial_messages=True,
                 )
                 return {
                     "success": True,
-                    "message": f"Successfully cleared conversation history for {target_user.name}. Messages from other users and system messages preserved.",
+                    "message": f"Successfully cleared conversation history for {target_user.name}.",
                     "messages_deleted": user_messages_count,
                 }
         except Exception as e:
             return {"success": False, "error": str(e), "messages_deleted": 0}
 
-    def save(self, path: Optional[str] = None) -> Dict[str, Any]:
-        """
-        Save the current memory state to disk.
-
-        Note: Save/backup functionality is not yet implemented in the client-based SDK.
-        Please use the database backup directly.
-
-        Args:
-            path: Save directory path (optional). If not provided, generates
-                 timestamp-based directory name.
-
-        Returns:
-            Dict containing success status and backup path
-
-        Example:
-            result = memory_agent.save("./my_backup")
-        """
-        return {
-            "success": False,
-            "error": "Save functionality not yet implemented in client-based SDK. Please backup the database directly.",
-            "path": path or "N/A",
-        }
-
-    def load(self, path: str) -> Dict[str, Any]:
-        """
-        Load memory state from a backup directory.
-
-        Note: Load/restore functionality is not yet implemented in the client-based SDK.
-        Please restore the database directly.
-
-        Args:
-            path: Path to backup directory
-
-        Returns:
-            Dict containing success status and any error messages
-
-        Example:
-            result = memory_agent.load("./my_backup")
-        """
-        return {
-            "success": False,
-            "error": "Load functionality not yet implemented in client-based SDK. Please restore the database directly.",
-        }
-
     def _reload_model_settings(self):
         """
         Force reload of model_settings to pick up new environment variables.
@@ -521,7 +434,9 @@ async def insert_tool(
             )
 
             # Use the tool manager's create_or_update_tool method
-            created_tool = await tool_manager.create_or_update_tool(pydantic_tool=pydantic_tool, actor=self._client.client)
+            created_tool = await tool_manager.create_or_update_tool(
+                pydantic_tool=pydantic_tool, actor=self._client.client
+            )
 
         # Apply tool to all existing agents if requested
         if apply_to_agents:
@@ -646,8 +561,6 @@ async def visualize_memories(self, user_id: Optional[str] = None) -> Dict[str, A
             if not target_user:
                 return {"success": False, "error": "No user found"}
 
-            meta_agent_state = await self._client.get_agent(self._meta_agent.id)
-
             memories = {}
 
             # Get episodic memory
diff --git a/mirix/server/rest_api.py b/mirix/server/rest_api.py
index 27f306802..92bec53a3 100644
--- a/mirix/server/rest_api.py
+++ b/mirix/server/rest_api.py
@@ -4,17 +4,15 @@
 allowing MirixClient instances to communicate with a cloud-hosted server.
 """
 
-import asyncio
-import copy
 import functools
 import json
 import traceback
 from contextlib import asynccontextmanager
 from datetime import datetime
-from typing import Any, Dict, List, Literal, Optional, Union
+from typing import Any, Dict, List, Optional
 
 import httpx
-from fastapi import APIRouter, Body, FastAPI, Header, HTTPException, Query, Request
+from fastapi import APIRouter, FastAPI, Header, HTTPException, Query, Request
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.responses import JSONResponse
 from pydantic import BaseModel, Field
@@ -24,43 +22,29 @@
 from mirix.log import get_logger
 from mirix.orm.errors import NoResultFound
 from mirix.schemas.agent import AgentState, AgentType, CreateAgent
-from mirix.schemas.block import Block, BlockUpdate, CreateBlock, Human, Persona
-from mirix.schemas.client import Client, ClientCreate, ClientUpdate
+from mirix.schemas.block import Block
+from mirix.schemas.client import Client, ClientUpdate
 from mirix.schemas.embedding_config import EmbeddingConfig
 from mirix.schemas.enums import MessageRole
-from mirix.schemas.environment_variables import (
-    SandboxEnvironmentVariable,
-    SandboxEnvironmentVariableCreate,
-    SandboxEnvironmentVariableUpdate,
-)
-from mirix.schemas.file import FileMetadata
 from mirix.schemas.llm_config import LLMConfig
-from mirix.schemas.memory import ArchivalMemorySummary, Memory, RecallMemorySummary
+from mirix.schemas.memory import Memory
 from mirix.schemas.message import Message, MessageCreate
 from mirix.schemas.mirix_response import MirixResponse
 from mirix.schemas.organization import Organization
 from mirix.schemas.procedural_memory import ProceduralMemoryItemUpdate
 from mirix.schemas.raw_memory import (
-    RawMemoryItem,
     RawMemoryItemCreateRequest,
     RawMemoryItemUpdate,
     SearchRawMemoryRequest,
     SearchRawMemoryResponse,
 )
 from mirix.schemas.resource_memory import ResourceMemoryItemUpdate
-from mirix.schemas.sandbox_config import (
-    E2BSandboxConfig,
-    LocalSandboxConfig,
-    SandboxConfig,
-    SandboxConfigCreate,
-    SandboxConfigUpdate,
-)
 from mirix.schemas.semantic_memory import SemanticMemoryItemUpdate
-from mirix.schemas.tool import Tool, ToolCreate, ToolUpdate
+from mirix.schemas.tool import Tool
 from mirix.schemas.tool_rule import BaseToolRule
 from mirix.schemas.user import User
 from mirix.server.server import AsyncServer, ensure_tables_created
-from mirix.settings import model_settings, settings
+from mirix.settings import model_settings
 from mirix.utils import convert_message_to_mirix_message
 
 logger = get_logger(__name__)
@@ -521,9 +505,7 @@ async def extract_topics_and_temporal_info(
     return None, None
 
 
-async def extract_topics_from_messages(
-    messages: List[Dict[str, Any]], llm_config: LLMConfig
-) -> Optional[str]:
+async def extract_topics_from_messages(messages: List[Dict[str, Any]], llm_config: LLMConfig) -> Optional[str]:
     """
     Extract topics from a list of messages using LLM.
 
@@ -570,9 +552,7 @@ def _flatten_messages_to_plain_text(messages: List[Dict[str, Any]]) -> str:
     return "\n".join(transcript_parts)
 
 
-async def extract_topics_with_local_model(
-    messages: List[Dict[str, Any]], model_name: str
-) -> Optional[str]:
+async def extract_topics_with_local_model(messages: List[Dict[str, Any]], model_name: str) -> Optional[str]:
     """
     Extract topics using a locally hosted Ollama model via the /api/chat endpoint.
 
@@ -729,7 +709,6 @@ class CreateAgentRequest(BaseModel):
     include_meta_memory_tools: Optional[bool] = False
     metadata: Optional[Dict] = None
     description: Optional[str] = None
-    initial_message_sequence: Optional[List[Message]] = None
     tags: Optional[List[str]] = None
 
 
@@ -767,20 +746,15 @@ async def create_agent(
         "agent_type": request.agent_type,
         "llm_config": request.llm_config,
         "embedding_config": request.embedding_config,
-        "initial_message_sequence": request.initial_message_sequence,
         "tags": request.tags,
     }
 
     if request.name:
         create_params["name"] = request.name
 
-    agent_state = await server.create_agent(
-        CreateAgent(**create_params), client
-    )
+    agent_state = await server.create_agent(CreateAgent(**create_params), client)
 
-    return await server.agent_manager.get_agent_by_id(
-        agent_state.id, client
-    )
+    return await server.agent_manager.get_agent_by_id(agent_state.id, client)
 
 
 @router.get("/agents/{agent_id}", response_model=AgentState)
@@ -797,10 +771,8 @@ async def get_agent(
     client = await server.client_manager.get_client_by_id(client_id)
 
     try:
-        return await server.agent_manager.get_agent_by_id(
-            agent_id, client
-        )
-    except NoResultFound as e:
+        return await server.agent_manager.get_agent_by_id(agent_id, client)
+    except NoResultFound:
         raise HTTPException(status_code=404, detail=f"Agent {agent_id} not found or not accessible")
 
 
@@ -828,7 +800,6 @@ class UpdateAgentRequest(BaseModel):
     metadata: Optional[Dict] = None
     llm_config: Optional[LLMConfig] = None
     embedding_config: Optional[EmbeddingConfig] = None
-    message_ids: Optional[List[str]] = None
     memory: Optional[Memory] = None
     tags: Optional[List[str]] = None
 
@@ -896,9 +867,7 @@ async def update_agent_system_prompt_by_name(
     client = await server.client_manager.get_client_by_id(client_id)
 
     # List all top-level agents for this client
-    top_level_agents = await server.agent_manager.list_agents(
-        actor=client, limit=1000
-    )
+    top_level_agents = await server.agent_manager.list_agents(actor=client, limit=1000)
     # Also get sub-agents (children of meta agent)
     all_agents = list(top_level_agents)
     for agent in top_level_agents:
@@ -985,8 +954,7 @@ async def update_agent_system_prompt(
     The update process:
     1. Updates the agent.system field in PostgreSQL
     2. Updates the agent.system field in Redis cache
-    3. Creates a new system message
-    4. Updates message_ids[0] to reference the new system message
+    3. Updates agent.system in DB and cache
 
     Args:
         agent_id: ID of the agent to update (e.g., "agent-123")
@@ -1119,9 +1087,7 @@ async def list_tools(
     server = get_server()
     client_id, org_id = await get_client_and_org(x_client_id, x_org_id)
     client = await server.client_manager.get_client_by_id(client_id)
-    return await server.tool_manager.list_tools(
-        cursor=cursor, limit=limit, actor=client
-    )
+    return await server.tool_manager.list_tools(cursor=cursor, limit=limit, actor=client)
 
 
 @router.get("/tools/{tool_id}", response_model=Tool)
@@ -1270,9 +1236,7 @@ async def list_organizations(
 ):
     """List organizations."""
     server = get_server()
-    return await server.organization_manager.list_organizations(
-        cursor=cursor, limit=limit
-    )
+    return await server.organization_manager.list_organizations(cursor=cursor, limit=limit)
 
 
 @router.post("/organizations", response_model=Organization)
@@ -1283,9 +1247,7 @@ async def create_organization(
 ):
     """Create an organization."""
     server = get_server()
-    return await server.organization_manager.create_organization(
-        pydantic_org=Organization(name=name)
-    )
+    return await server.organization_manager.create_organization(pydantic_org=Organization(name=name))
 
 
 @router.get("/organizations/{org_id}", response_model=Organization)
@@ -1342,9 +1304,7 @@ async def create_or_get_organization(
 
     # Create new organization if it doesn't exist
     org_create = OrganizationCreate(id=org_id, name=request.name or org_id)
-    org = await server.organization_manager.create_organization(
-        pydantic_org=Organization(**org_create.model_dump())
-    )
+    org = await server.organization_manager.create_organization(pydantic_org=Organization(**org_create.model_dump()))
     logger.debug("Created new organization: %s", org_id)
     return org
 
@@ -1890,7 +1850,7 @@ async def delete_client_api_key(
             "message": f"API key {api_key_id} deleted successfully",
             "id": api_key_id,
         }
-    except Exception as e:
+    except Exception:
         raise HTTPException(status_code=404, detail=f"API key {api_key_id} not found")
 
 
@@ -1947,9 +1907,7 @@ async def initialize_meta_agent(
 
     # Check if meta agent already exists for this client
     # list_agents now automatically filters by client (organization_id + _created_by_id)
-    existing_meta_agents = await server.agent_manager.list_agents(
-        actor=client, limit=1000
-    )
+    existing_meta_agents = await server.agent_manager.list_agents(actor=client, limit=1000)
 
     assert len(existing_meta_agents) <= 1, "Only one meta agent can be created per client"
 
@@ -2077,6 +2035,8 @@ async def add_memory(
                 raise ValueError(f"Invalid content type: {type(content)}")
         message = new_message
 
+    # N.b. This function converts to Mirix format and also packs all messages into a single MessageCreate object
+    # so, there will be only one MessageCreate object in the list
     input_messages = convert_message_to_mirix_message(message)
 
     # Add client scope to filter_tags (create if not provided)
@@ -2438,9 +2398,7 @@ async def retrieve_memory_with_conversation(
     filter_tags = dict(request.filter_tags) if request.filter_tags is not None else {}
 
     # Get all agents for this client (automatically filtered by client via apply_access_predicate)
-    all_agents = await server.agent_manager.list_agents(
-        actor=client, limit=1000
-    )
+    all_agents = await server.agent_manager.list_agents(actor=client, limit=1000)
 
     if not all_agents:
         return {
@@ -2484,9 +2442,7 @@ async def retrieve_memory_with_conversation(
 
         if topics is None:
             # NEW: Extract both topics and temporal expression
-            topics, temporal_expr = await extract_topics_and_temporal_info(
-                request.messages, llm_config
-            )
+            topics, temporal_expr = await extract_topics_and_temporal_info(request.messages, llm_config)
 
         logger.debug("Extracted topics: %s, temporal: %s", topics, temporal_expr)
         key_words = topics if topics else ""
@@ -2620,9 +2576,7 @@ async def retrieve_memory_with_topic(
         parsed_filter_tags = {}
 
     # Get all agents for this client (automatically filtered by client via apply_access_predicate)
-    all_agents = await server.agent_manager.list_agents(
-        actor=client, limit=1000
-    )
+    all_agents = await server.agent_manager.list_agents(actor=client, limit=1000)
 
     if not all_agents:
         return {
@@ -2763,9 +2717,7 @@ async def search_memory(
         logger.debug("No user_id provided, using admin user: %s", user_id)
 
     # Get all agents for this client (automatically filtered by client via apply_access_predicate)
-    all_agents = await server.agent_manager.list_agents(
-        actor=client, limit=1000
-    )
+    all_agents = await server.agent_manager.list_agents(actor=client, limit=1000)
 
     if not all_agents:
         return {
@@ -3376,9 +3328,7 @@ async def search_memory_all_users(
             logger.warning("Invalid end_date format: %s", e)
 
     # Get agents for this client
-    all_agents = await server.agent_manager.list_agents(
-        actor=client, limit=1000
-    )
+    all_agents = await server.agent_manager.list_agents(actor=client, limit=1000)
     if not all_agents:
         return {
             "success": False,
@@ -3884,9 +3834,7 @@ async def list_memory_components(
     limit = max(1, min(limit, 200))  # guardrails
 
     # Need an agent state for memory manager configuration
-    agents = await server.agent_manager.list_agents(
-        actor=client, limit=1
-    )
+    agents = await server.agent_manager.list_agents(actor=client, limit=1)
     if not agents:
         raise HTTPException(status_code=404, detail="No agents found for this client")
     agent_state = agents[0]
@@ -4446,9 +4394,7 @@ async def create_raw_memory(
         raise HTTPException(status_code=401, detail="Client or client_id required")
 
     # Get agent_state for embedding generation (required)
-    agents = await server.agent_manager.list_agents(
-        actor=client, limit=1
-    )
+    agents = await server.agent_manager.list_agents(actor=client, limit=1)
     agent_state = agents[0] if agents else None
 
     if not agent_state:
@@ -4623,9 +4569,7 @@ async def update_raw_memory(
             raise HTTPException(status_code=404, detail=f"User {user_id} not found")
 
     # Get agent_state for embedding generation (required)
-    agents = await server.agent_manager.list_agents(
-        actor=client, limit=1
-    )
+    agents = await server.agent_manager.list_agents(actor=client, limit=1)
     agent_state = agents[0] if agents else None
 
     if not agent_state:
@@ -5242,9 +5186,7 @@ async def dashboard_login(request: DashboardLoginRequest):
 
     auth_manager = ClientAuthManager()
 
-    client, access_token, auth_status = await auth_manager.authenticate(
-        request.email, request.password
-    )
+    client, access_token, auth_status = await auth_manager.authenticate(request.email, request.password)
 
     if auth_status == "not_found":
         raise HTTPException(status_code=404, detail="Account does not exist. Please create an account.")
diff --git a/mirix/server/server.py b/mirix/server/server.py
index 3a200188c..6a7ed9ebd 100644
--- a/mirix/server/server.py
+++ b/mirix/server/server.py
@@ -1,7 +1,6 @@
 # inspecting tools
 import asyncio
 import os
-import sys
 import traceback
 import warnings
 from abc import abstractmethod
@@ -16,9 +15,7 @@
 from rich.console import Console
 from rich.panel import Panel
 from rich.text import Text
-from sqlalchemy import create_engine
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
-from sqlalchemy.orm import sessionmaker
 
 import mirix.constants as constants
 import mirix.server.utils as server_utils
@@ -34,7 +31,6 @@
     ReflexionAgent,
     ResourceMemoryAgent,
     SemanticMemoryAgent,
-    save_agent,
 )
 from mirix.config import MirixConfig
 
@@ -45,14 +41,14 @@
 from mirix.log import get_logger
 from mirix.orm import Base
 from mirix.orm.errors import NoResultFound
-from mirix.schemas.agent import AgentState, AgentType, CreateAgent, CreateMetaAgent
+from mirix.schemas.agent import AgentState, AgentType, CreateAgent
 from mirix.schemas.client import Client
 from mirix.schemas.embedding_config import EmbeddingConfig
 
 # openai schemas
 from mirix.schemas.enums import MessageStreamStatus
 from mirix.schemas.llm_config import LLMConfig
-from mirix.schemas.memory import ContextWindowOverview, RecallMemorySummary
+from mirix.schemas.memory import RecallMemorySummary
 from mirix.schemas.message import Message, MessageCreate, MessageUpdate
 from mirix.schemas.mirix_message import LegacyMirixMessage, MirixMessage, ToolReturnMessage
 from mirix.schemas.mirix_response import MirixResponse
@@ -311,7 +307,7 @@ async def __call__(self):
 
     # asyncpg does not accept 'sslmode' as a keyword argument — strip it from
     # the URI and pass an ssl.SSLContext via connect_args instead.
-    from urllib.parse import urlparse, parse_qs, urlencode, urlunparse
+    from urllib.parse import parse_qs, urlencode, urlparse, urlunparse
 
     _parsed = urlparse(_pg_uri)
     _params = parse_qs(_parsed.query, keep_blank_values=True)
@@ -432,6 +428,7 @@ async def get_db():
     def db_context():
         """Async context manager for service managers (PGlite)."""
         return pglite_session_factory()
+
 else:
 
     async def get_db():
@@ -645,9 +642,7 @@ async def load_agent(
         """Updated method to load agents from persisted storage."""
         agent_lock = self.per_agent_lock_manager.get_lock(agent_id)
         async with agent_lock:
-            agent_state = await self.agent_manager.get_agent_by_id(
-                agent_id=agent_id, actor=actor
-            )
+            agent_state = await self.agent_manager.get_agent_by_id(agent_id=agent_id, actor=actor)
 
             common_kwargs = dict(
                 interface=interface or self.default_interface_factory(),
@@ -705,6 +700,8 @@ async def _step(
     ) -> MirixUsageStatistics:
         """Send the input message through the agent"""
         logger.debug("Got input messages: %s", input_messages)
+        if user is None:
+            raise ValueError("AsyncServer._step requires a non-null user.")
         mirix_agent = None
         try:
             mirix_agent = await self.load_agent(
@@ -783,9 +780,6 @@ async def _command(self, user_id: str, agent_id: str, command: str) -> MirixUsag
             # exit not supported on server.py
             raise ValueError(command)
 
-        elif command.lower() == "save" or command.lower() == "savechat":
-            await save_agent(mirix_agent)
-
         elif command.lower() == "dump" or command.lower().startswith("dump "):
             # Check if there's an additional argument that's an integer
             command = command.strip().split()
@@ -867,11 +861,11 @@ async def _command(self, user_id: str, agent_id: str, command: str) -> MirixUsag
 
         elif command.lower() == "contine_chaining":
             input_message = system.get_contine_chaining()
-            usage = await self._step(actor=actor, agent_id=agent_id, input_messages=input_message)
+            usage = await self._step(actor=actor, agent_id=agent_id, input_messages=input_message, user=actor)
 
         elif command.lower() == "memorywarning":
             input_message = system.get_token_limit_warning()
-            usage = await self._step(actor=actor, agent_id=agent_id, input_messages=input_message)
+            usage = await self._step(actor=actor, agent_id=agent_id, input_messages=input_message, user=actor)
 
         if not usage:
             usage = MirixUsageStatistics()
@@ -927,7 +921,7 @@ async def user_message(
                 )
 
         # Run the agent state forward
-        usage = await self._step(actor=actor, agent_id=agent_id, input_messages=message)
+        usage = await self._step(actor=actor, agent_id=agent_id, input_messages=message, user=actor)
         return usage
 
     async def system_message(
@@ -992,7 +986,7 @@ async def system_message(
             message.created_at = timestamp
 
         # Run the agent state forward
-        return await self._step(actor=actor, agent_id=agent_id, input_messages=message)
+        return await self._step(actor=actor, agent_id=agent_id, input_messages=message, user=actor)
 
     async def construct_system_message(self, agent_id: str, message: str, actor: Client) -> str:
         """
@@ -1055,6 +1049,9 @@ async def send_messages(
 
             set_verbose(verbose)
 
+        if user is None:
+            user = await self.user_manager.get_admin_user()
+
         try:
             # Run the agent state forward
             return await self._step(
@@ -1292,10 +1289,6 @@ def add_llm_model(self, request: LLMConfig) -> LLMConfig:
     def add_embedding_model(self, request: EmbeddingConfig) -> EmbeddingConfig:
         """Add a new embedding model"""
 
-    async def get_agent_context_window(self, agent_id: str, actor: Client) -> ContextWindowOverview:
-        mirix_agent = await self.load_agent(agent_id=agent_id, actor=actor)
-        return await mirix_agent.get_context_window()
-
     async def run_tool_from_source(
         self,
         actor: Client,
diff --git a/mirix/services/admin_user_manager.py b/mirix/services/admin_user_manager.py
index 1b4a706d9..5872b8628 100644
--- a/mirix/services/admin_user_manager.py
+++ b/mirix/services/admin_user_manager.py
@@ -278,9 +278,7 @@ async def register_client_for_dashboard(
             return client.to_pydantic()
 
     @enforce_types
-    async def authenticate(
-        self, email: str, password: str
-    ) -> Tuple[Optional[PydanticClient], Optional[str], str]:
+    async def authenticate(self, email: str, password: str) -> Tuple[Optional[PydanticClient], Optional[str], str]:
         """
         Authenticate a client for dashboard access and return client + JWT token.
 
@@ -310,27 +308,19 @@ async def authenticate(
             client = result.scalar_one_or_none()
 
             if not client:
-                logger.warning(
-                    "Login attempt for non-existent email: %s", email
-                )
+                logger.warning("Login attempt for non-existent email: %s", email)
                 return None, None, "not_found"
 
             if client.status != "active":
-                logger.warning(
-                    "Login attempt for inactive client: %s", email
-                )
+                logger.warning("Login attempt for inactive client: %s", email)
                 return None, None, "inactive"
 
             if not client.password_hash:
-                logger.warning(
-                    "Login attempt for client without password: %s", email
-                )
+                logger.warning("Login attempt for client without password: %s", email)
                 return None, None, "no_password"
 
             if not self.verify_password(password, client.password_hash):
-                logger.warning(
-                    "Failed login attempt for client: %s", email
-                )
+                logger.warning("Failed login attempt for client: %s", email)
                 return None, None, "wrong_password"
 
             client.last_login = datetime.now(timezone.utc)
@@ -347,9 +337,7 @@ async def get_client_by_id(self, client_id: str) -> Optional[PydanticClient]:
         """Get a client by ID."""
         async with self.session_maker() as session:
             try:
-                client = await ClientModel.read(
-                    db_session=session, identifier=client_id
-                )
+                client = await ClientModel.read(db_session=session, identifier=client_id)
                 if client.is_deleted:
                     return None
                 return client.to_pydantic()
@@ -375,9 +363,7 @@ async def get_client_by_email(self, email: str) -> Optional[PydanticClient]:
             return None
 
     @enforce_types
-    async def list_dashboard_clients(
-        self, cursor: Optional[str] = None, limit: int = 50
-    ) -> List[PydanticClient]:
+    async def list_dashboard_clients(self, cursor: Optional[str] = None, limit: int = 50) -> List[PydanticClient]:
         """List all clients that have dashboard access (email set)."""
         async with self.session_maker() as session:
             stmt = (
@@ -397,9 +383,7 @@ async def list_dashboard_clients(
             return [client.to_pydantic() for client in clients]
 
     @enforce_types
-    async def set_client_password(
-        self, client_id: str, email: str, password: str
-    ) -> PydanticClient:
+    async def set_client_password(self, client_id: str, email: str, password: str) -> PydanticClient:
         """
         Set dashboard credentials for an existing client.
 
@@ -412,9 +396,7 @@ async def set_client_password(
             Updated client
         """
         async with self.session_maker() as session:
-            client = await ClientModel.read(
-                db_session=session, identifier=client_id
-            )
+            client = await ClientModel.read(db_session=session, identifier=client_id)
 
             if client.is_deleted:
                 raise ValueError("Cannot update deleted client")
@@ -430,9 +412,7 @@ async def set_client_password(
             )
             result = await session.execute(stmt)
             if result.scalar_one_or_none():
-                raise ValueError(
-                    f"Email '{email}' already exists on another client"
-                )
+                raise ValueError(f"Email '{email}' already exists on another client")
 
             client.email = email.lower()
             client.password_hash = self.hash_password(password)
@@ -442,9 +422,7 @@ async def set_client_password(
             return client.to_pydantic()
 
     @enforce_types
-    async def change_password(
-        self, client_id: str, current_password: str, new_password: str
-    ) -> bool:
+    async def change_password(self, client_id: str, current_password: str, new_password: str) -> bool:
         """
         Change a client's dashboard password.
 
@@ -457,9 +435,7 @@ async def change_password(
             True if successful, False otherwise
         """
         async with self.session_maker() as session:
-            client = await ClientModel.read(
-                db_session=session, identifier=client_id
-            )
+            client = await ClientModel.read(db_session=session, identifier=client_id)
 
             if not client.password_hash:
                 logger.warning(
@@ -468,9 +444,7 @@ async def change_password(
                 )
                 return False
 
-            if not self.verify_password(
-                current_password, client.password_hash
-            ):
+            if not self.verify_password(current_password, client.password_hash):
                 logger.warning(
                     "Password change failed: incorrect current password for %s",
                     client_id,
@@ -489,9 +463,13 @@ async def count_dashboard_clients(self) -> int:
         from sqlalchemy import func
 
         async with self.session_maker() as session:
-            stmt = select(func.count()).select_from(ClientModel).where(
-                ClientModel.is_deleted == False,
-                ClientModel.email.isnot(None),
+            stmt = (
+                select(func.count())
+                .select_from(ClientModel)
+                .where(
+                    ClientModel.is_deleted == False,
+                    ClientModel.email.isnot(None),
+                )
             )
             result = await session.execute(stmt)
             return result.scalar() or 0
diff --git a/mirix/services/agent_manager.py b/mirix/services/agent_manager.py
index 3250146e6..6c5a856b2 100644
--- a/mirix/services/agent_manager.py
+++ b/mirix/services/agent_manager.py
@@ -22,19 +22,20 @@
 )
 from mirix.log import get_logger
 from mirix.orm import Agent as AgentModel
-from mirix.orm import Block as BlockModel
 from mirix.orm import Tool as ToolModel
 from mirix.orm.errors import NoResultFound
+
+logger = get_logger(__name__)
+
+# Diagnostic flag for MissingGreenlet debugging
+
+_TRACE_MISSING_GREENLET = os.getenv("MIRIX_TRACE_MISSING_GREENLET", "false").lower() == "true"
 from mirix.schemas.agent import AgentState as PydanticAgentState
 from mirix.schemas.agent import AgentType, CreateAgent, CreateMetaAgent, UpdateAgent, UpdateMetaAgent
-from mirix.schemas.block import Block
-from mirix.schemas.block import Block as PydanticBlock
 from mirix.schemas.client import Client as PydanticClient
 from mirix.schemas.embedding_config import EmbeddingConfig
 from mirix.schemas.enums import ToolType
 from mirix.schemas.llm_config import LLMConfig
-from mirix.schemas.message import Message as PydanticMessage
-from mirix.schemas.message import MessageCreate
 from mirix.schemas.tool_rule import ToolRule as PydanticToolRule
 from mirix.schemas.user import User as PydanticUser
 from mirix.services.block_manager import BlockManager
@@ -42,13 +43,11 @@
     _process_relationship,
     check_supports_structured_output,
     derive_system_message,
-    initialize_message_sequence,
-    package_initial_message_sequence,
 )
 from mirix.services.message_manager import MessageManager
 from mirix.services.tool_manager import ToolManager
 from mirix.services.user_manager import UserManager
-from mirix.utils import create_random_username, enforce_types, get_utc_time
+from mirix.utils import create_random_username, enforce_types
 
 logger = get_logger(__name__)
 
@@ -165,9 +164,7 @@ async def create_agent(
             actor=actor,
         )
 
-        return await self.append_initial_message_sequence_to_in_context_messages(
-            actor, agent_state, agent_create.initial_message_sequence
-        )
+        return agent_state
 
     async def create_meta_agent(
         self,
@@ -404,7 +401,7 @@ async def update_meta_agent(
             )
             meta_agent_state = await self.get_agent_by_id(agent_id=meta_agent_id, actor=actor)
 
-        # Update meta agent's system prompt if provided (separate call needed for rebuild_system_prompt)
+        # Update meta agent's system prompt if provided
         if meta_agent_update.system_prompts and "meta_memory_agent" in meta_agent_update.system_prompts:
             await self.update_system_prompt(
                 agent_id=meta_agent_id,
@@ -627,62 +624,6 @@ async def update_agent_tools_and_system_prompts(
                 actor=actor,
             )
 
-    @enforce_types
-    def _generate_initial_message_sequence(
-        self,
-        actor: PydanticClient,
-        agent_state: PydanticAgentState,
-        supplied_initial_message_sequence: Optional[List[MessageCreate]] = None,
-        user_id: Optional[str] = None,
-    ) -> List[PydanticMessage]:
-        init_messages = initialize_message_sequence(
-            agent_state=agent_state,
-            memory_edit_timestamp=get_utc_time(),
-            include_initial_boot_message=True,
-        )
-        if supplied_initial_message_sequence is not None:
-            # We always need the system prompt up front
-            system_message_obj = PydanticMessage.dict_to_message(
-                agent_id=agent_state.id,
-                model=agent_state.llm_config.model,
-                openai_message_dict=init_messages[0],
-            )
-            # Don't use anything else in the pregen sequence, instead use the provided sequence
-            init_messages = [system_message_obj]
-            init_messages.extend(
-                package_initial_message_sequence(
-                    agent_state.id,
-                    supplied_initial_message_sequence,
-                    agent_state.llm_config.model,
-                    actor,
-                    user_id=user_id,
-                )
-            )
-        else:
-            init_messages = [
-                PydanticMessage.dict_to_message(
-                    agent_id=agent_state.id,
-                    model=agent_state.llm_config.model,
-                    openai_message_dict=msg,
-                )
-                for msg in init_messages
-            ]
-
-        return init_messages
-
-    @enforce_types
-    async def append_initial_message_sequence_to_in_context_messages(
-        self,
-        actor: PydanticClient,
-        agent_state: PydanticAgentState,
-        initial_message_sequence: Optional[List[MessageCreate]] = None,
-        user_id: Optional[str] = None,
-    ) -> PydanticAgentState:
-        init_messages = self._generate_initial_message_sequence(
-            actor, agent_state, initial_message_sequence, user_id=user_id
-        )
-        return await self.append_to_in_context_messages(init_messages, agent_id=agent_state.id, actor=actor, user_id=user_id)
-
     @enforce_types
     async def _create_agent(
         self,
@@ -728,27 +669,13 @@ async def _create_agent(
 
     @enforce_types
     async def update_agent(self, agent_id: str, agent_update: UpdateAgent, actor: PydanticClient) -> PydanticAgentState:
-        # Get current state BEFORE update to detect changes
-        old_agent_state = None
-        if agent_update.system:
-            old_agent_state = await self.get_agent_by_id(agent_id=agent_id, actor=actor)
-
-        # Update agent (including system field in database)
-        agent_state = await self._update_agent(agent_id=agent_id, agent_update=agent_update, actor=actor)
-
-        # Rebuild the system prompt if it changed
-        if agent_update.system and old_agent_state and agent_update.system != old_agent_state.system:
-            agent_state = await self.rebuild_system_prompt(
-                agent_id=agent_state.id,
-                system_prompt=agent_update.system,  # Pass the new system prompt
-                actor=actor,
-                force=True,
-            )
-
-        return agent_state
+        # Update agent (system prompt and all other fields are persisted directly)
+        return await self._update_agent(agent_id=agent_id, agent_update=agent_update, actor=actor)
 
     @enforce_types
-    async def update_llm_config(self, agent_id: str, llm_config: LLMConfig, actor: PydanticClient) -> PydanticAgentState:
+    async def update_llm_config(
+        self, agent_id: str, llm_config: LLMConfig, actor: PydanticClient
+    ) -> PydanticAgentState:
         return await self.update_agent(
             agent_id=agent_id,
             agent_update=UpdateAgent(llm_config=llm_config),
@@ -756,20 +683,14 @@ async def update_llm_config(self, agent_id: str, llm_config: LLMConfig, actor: P
         )
 
     @enforce_types
-    async def update_system_prompt(self, agent_id: str, system_prompt: str, actor: PydanticClient) -> PydanticAgentState:
-        agent_state = await self.update_agent(
+    async def update_system_prompt(
+        self, agent_id: str, system_prompt: str, actor: PydanticClient
+    ) -> PydanticAgentState:
+        return await self.update_agent(
             agent_id=agent_id,
             agent_update=UpdateAgent(system=system_prompt),
             actor=actor,
         )
-        # Rebuild the system prompt if it's different
-        agent_state = await self.rebuild_system_prompt(
-            agent_id=agent_state.id,
-            system_prompt=system_prompt,
-            actor=actor,
-            force=True,
-        )
-        return agent_state
 
     @enforce_types
     async def update_mcp_tools(
@@ -812,7 +733,9 @@ async def add_mcp_tool(
         return agent_state
 
     @enforce_types
-    async def _update_agent(self, agent_id: str, agent_update: UpdateAgent, actor: PydanticClient) -> PydanticAgentState:
+    async def _update_agent(
+        self, agent_id: str, agent_update: UpdateAgent, actor: PydanticClient
+    ) -> PydanticAgentState:
         """
         Update an existing agent.
 
@@ -837,7 +760,6 @@ async def _update_agent(self, agent_id: str, agent_update: UpdateAgent, actor: P
                 "system",
                 "llm_config",
                 "embedding_config",
-                "message_ids",
                 "tool_rules",
                 "mcp_tools",
                 "parent_id",
@@ -984,12 +906,6 @@ async def _reconstruct_children_from_cache(
                     continue
 
                 # Deserialize JSON fields
-                if "message_ids" in child_data:
-                    child_data["message_ids"] = (
-                        json.loads(child_data["message_ids"])
-                        if isinstance(child_data["message_ids"], (str, bytes))
-                        else child_data["message_ids"]
-                    )
                 if "llm_config" in child_data:
                     child_data["llm_config"] = (
                         json.loads(child_data["llm_config"])
@@ -1108,7 +1024,9 @@ async def _get_children_from_db(self, parent_ids: List[str], session: Session, a
         )
         return children_by_parent
 
-    async def _get_children_from_redis(self, parent_id: str, actor: PydanticClient) -> Optional[List[PydanticAgentState]]:
+    async def _get_children_from_redis(
+        self, parent_id: str, actor: PydanticClient
+    ) -> Optional[List[PydanticAgentState]]:
         """
         Fetch children from Redis cache using parent's children_ids.
 
@@ -1261,7 +1179,25 @@ async def list_agents(
             )
 
             # Convert to Pydantic
-            agent_states = [agent.to_pydantic() for agent in agents]
+            if _TRACE_MISSING_GREENLET:
+                logger.info("Converting %d agents to Pydantic in list_agents", len(agents))
+                agent_states = []
+                for i, agent in enumerate(agents):
+                    try:
+                        agent_states.append(agent.to_pydantic())
+                    except Exception as e:
+                        if "MissingGreenlet" in str(type(e).__name__) or "greenlet" in str(e).lower():
+                            import traceback
+
+                            logger.error(
+                                "MissingGreenlet in list_agents at index %d, agent_id=%s\n" "Full traceback:\n%s",
+                                i,
+                                agent.id,
+                                traceback.format_exc(),
+                            )
+                        raise
+            else:
+                agent_states = [agent.to_pydantic() for agent in agents]
 
             # If there are no agents, return early
             if not agent_states:
@@ -1302,12 +1238,6 @@ async def get_agent_by_id(self, agent_id: str, actor: PydanticClient) -> Pydanti
                     logger.debug("Cache HIT for agent %s", agent_id)
 
                     # Deserialize JSON fields
-                    if "message_ids" in cached_data:
-                        cached_data["message_ids"] = (
-                            json.loads(cached_data["message_ids"])
-                            if isinstance(cached_data["message_ids"], str)
-                            else cached_data["message_ids"]
-                        )
                     if "llm_config" in cached_data:
                         cached_data["llm_config"] = (
                             json.loads(cached_data["llm_config"])
@@ -1388,7 +1318,23 @@ async def get_agent_by_id(self, agent_id: str, actor: PydanticClient) -> Pydanti
                 identifier=agent_id,
                 actor=actor,  # Triggers client-level filtering via apply_access_predicate
             )
-            pydantic_agent = agent.to_pydantic()
+
+            if _TRACE_MISSING_GREENLET:
+                try:
+                    logger.info("Converting agent %s to Pydantic in get_agent_by_id", agent_id)
+                    pydantic_agent = agent.to_pydantic()
+                except Exception as e:
+                    if "MissingGreenlet" in str(type(e).__name__) or "greenlet" in str(e).lower():
+                        import traceback
+
+                        logger.error(
+                            "MissingGreenlet in get_agent_by_id for agent_id=%s\n" "Full traceback:\n%s",
+                            agent_id,
+                            traceback.format_exc(),
+                        )
+                    raise
+            else:
+                pydantic_agent = agent.to_pydantic()
 
             # Populate cache for next time
             try:
@@ -1397,8 +1343,6 @@ async def get_agent_by_id(self, agent_id: str, actor: PydanticClient) -> Pydanti
 
                     data = pydantic_agent.model_dump(mode="json")
 
-                    if "message_ids" in data and data["message_ids"]:
-                        data["message_ids"] = json.dumps(data["message_ids"])
                     if "llm_config" in data and data["llm_config"]:
                         data["llm_config"] = json.dumps(data["llm_config"])
                     if "embedding_config" in data and data["embedding_config"]:
@@ -1495,185 +1439,17 @@ async def delete_agent(self, agent_id: str, actor: PydanticClient) -> None:
                 await self._invalidate_parent_cache_for_child(agent_id, parent_id)
 
     # ======================================================================================================================
-    # In Context Messages Management
+    # Message Management
     # ======================================================================================================================
-    # TODO: There are several assumptions here that are not explicitly checked
-    # TODO: 1) These message ids are valid
-    # TODO: 2) These messages are ordered from oldest to newest
-    # TODO: This can be fixed by having an actual relationship in the ORM for message_ids
-    # TODO: This can also be made more efficient, instead of getting, setting, we can do it all in one db session for one query.
-    # @enforce_types
-    # def get_in_context_messages(
-    #     self, agent_id: str, actor: PydanticClient
-    # ) -> List[PydanticMessage]:
-    #     message_ids = await self.get_agent_by_id(agent_id=agent_id, actor=actor).message_ids
-    #     messages = self.message_manager.get_messages_by_ids(
-    #         message_ids=message_ids, actor=actor
-    #     )
-    #     messages = [messages[0]] + [
-    #         message for message in messages[1:] if message.user_id == actor.id
-    #     ]
-    #     return messages
-    @enforce_types
-    async def get_in_context_messages(
-        self,
-        agent_state: PydanticAgentState,
-        actor: PydanticClient,
-        user: Optional[PydanticUser] = None,
-    ) -> List[PydanticMessage]:
-        message_ids = agent_state.message_ids
-        messages = await self.message_manager.get_messages_by_ids(message_ids=message_ids, actor=actor)
-        # Handle empty message list (e.g., after deletion)
-        if not messages:
-            return []
-
-        # Keep first message (system message) and filter rest by user_id
-        if user:
-            messages = [messages[0]] + [message for message in messages[1:] if message.user_id == user.id]
-        return messages
-
-    @enforce_types
-    async def get_system_message(self, agent_id: str, actor: PydanticClient) -> PydanticMessage:
-        agent_state = await self.get_agent_by_id(agent_id=agent_id, actor=actor)
-        message_ids = agent_state.message_ids
-
-        # Handle empty message_ids (e.g., after deletion)
-        if not message_ids:
-            return None
-
-        return await self.message_manager.get_message_by_id(message_id=message_ids[0], actor=actor)
-
-    @enforce_types
-    async def rebuild_system_prompt(
-        self, agent_id: str, system_prompt: str, actor: PydanticClient, force=False
-    ) -> PydanticAgentState:
-        """Rebuld the system prompt, put the system_prompt at the first position in the list of messages."""
-
-        agent_state = await self.get_agent_by_id(agent_id=agent_id, actor=actor)
-        # Swap the system message out (only if there is a diff)
-        message = PydanticMessage.dict_to_message(
-            agent_id=agent_id,
-            model=agent_state.llm_config.model,
-            openai_message_dict={"role": "system", "content": system_prompt},
-        )
-        message = await self.message_manager.create_message(message, actor=actor)
-        message_ids = [message.id] + agent_state.message_ids[1:]  # swap index 0 (system)
-        return await self.set_in_context_messages(agent_id=agent_id, message_ids=message_ids, actor=actor)
-
-    @enforce_types
-    async def set_in_context_messages(
-        self, agent_id: str, message_ids: List[str], actor: PydanticClient
-    ) -> PydanticAgentState:
-        return await self.update_agent(
-            agent_id=agent_id,
-            agent_update=UpdateAgent(message_ids=message_ids),
-            actor=actor,
-        )
-
-    @enforce_types
-    async def trim_older_in_context_messages(
-        self,
-        num: int,
-        agent_id: str,
-        actor: PydanticClient,
-        user_id: Optional[str] = None,
-    ) -> PydanticAgentState:
-        """
-        Trim older messages from the in-context message list, keeping `num` most recent messages
-        for the specified user. Messages from other users are preserved.
-
-        Args:
-            num: Number of most recent user messages to keep.
-            agent_id: The agent ID.
-            actor: The Client performing the operation.
-            user_id: The user whose messages to trim. If None, trims all non-system messages.
-        """
-        message_ids = await self.get_agent_by_id(agent_id=agent_id, actor=actor).message_ids
-        system_message_id = message_ids[0]
-        message_ids = message_ids[1:]
-
-        message_id_indices_belonging_to_user = []
-        for idx, message_id in enumerate(message_ids):
-            msg = await self.message_manager.get_message_by_id(message_id=message_id, actor=actor)
-            if msg and msg.user_id == user_id:
-                message_id_indices_belonging_to_user.append(idx)
-        message_ids_belonging_to_user = [message_ids[idx] for idx in message_id_indices_belonging_to_user]
-        message_ids_to_keep = [message_ids[idx] for idx in message_id_indices_belonging_to_user[num - 1 :]]
-
-        message_ids_belonging_to_user = set(message_ids_belonging_to_user)
-        message_ids_to_keep = set(message_ids_to_keep)
-
-        # new_messages = [message_ids[0]] + message_ids[num:]  # 0 is system message
-        new_messages = [system_message_id] + [
-            msg_id
-            for msg_id in message_ids
-            if (msg_id not in message_ids_belonging_to_user or msg_id in message_ids_to_keep)
-        ]
-        return await self.set_in_context_messages(agent_id=agent_id, message_ids=new_messages, actor=actor)
-
-    @enforce_types
-    async def trim_all_in_context_messages_except_system(
-        self, agent_id: str, actor: PydanticClient, user_id: Optional[str] = None
-    ) -> PydanticAgentState:
-        """
-        Remove all messages except the system message for a specific user.
-        Messages from other users are preserved.
-
-        Args:
-            agent_id: The agent ID.
-            actor: The Client performing the operation.
-            user_id: The user whose messages to remove. If None, removes all non-system messages.
-        """
-        message_ids = await self.get_agent_by_id(agent_id=agent_id, actor=actor).message_ids
-        system_message_id = message_ids[0]  # 0 is system message
-
-        # Keep system message and only filter out messages belonging to the specified user
-        new_message_ids = [system_message_id]
-        for message_id in message_ids[1:]:  # Skip system message
-            message = await self.message_manager.get_message_by_id(message_id=message_id, actor=actor)
-            if message.user_id != user_id:
-                new_message_ids.append(message_id)
-
-        return await self.set_in_context_messages(agent_id=agent_id, message_ids=new_message_ids, actor=actor)
-
-    @enforce_types
-    async def prepend_to_in_context_messages(
-        self,
-        messages: List[PydanticMessage],
-        agent_id: str,
-        actor: PydanticClient,
-        user_id: Optional[str] = None,
-    ) -> PydanticAgentState:
-        message_ids = await self.get_agent_by_id(agent_id=agent_id, actor=actor).message_ids
-        new_messages = await self.message_manager.create_many_messages(messages, actor=actor, user_id=user_id)
-        message_ids = [message_ids[0]] + [m.id for m in new_messages] + message_ids[1:]
-        return await self.set_in_context_messages(agent_id=agent_id, message_ids=message_ids, actor=actor)
-
-    @enforce_types
-    async def append_to_in_context_messages(
-        self,
-        messages: List[PydanticMessage],
-        agent_id: str,
-        actor: PydanticClient,
-        user_id: Optional[str] = None,
-    ) -> PydanticAgentState:
-        messages = await self.message_manager.create_many_messages(messages, actor=actor, user_id=user_id)
-        agent_state = await self.get_agent_by_id(agent_id=agent_id, actor=actor)
-        message_ids = list(agent_state.message_ids or [])
-        message_ids += [m.id for m in messages]
-        return await self.set_in_context_messages(agent_id=agent_id, message_ids=message_ids, actor=actor)
-
     @enforce_types
     async def reset_messages(
         self,
         agent_id: str,
         actor: PydanticClient,
         user_id: Optional[str] = None,
-        add_default_initial_messages: bool = False,
     ) -> PydanticAgentState:
         """
         Removes messages belonging to the specified user from the agent's conversation history.
-        Preserves system messages and messages from other users.
 
         This action is destructive and cannot be undone once committed.
 
@@ -1681,63 +1457,35 @@ async def reset_messages(
             agent_id (str): The ID of the agent whose messages will be reset.
             actor (PydanticClient): The Client performing this action.
             user_id (str): The user whose messages will be removed. If None, removes all non-system messages.
-            add_default_initial_messages: If true, adds the default initial messages after resetting.
 
         Returns:
-            PydanticAgentState: The updated agent state with user's messages removed.
+            PydanticAgentState: The updated agent state.
         """
-        async with self.session_maker() as session:
-            # Retrieve the existing agent (will raise NoResultFound if invalid)
-            agent = await AgentModel.read(db_session=session, identifier=agent_id, actor=actor)
-
-            # Get current messages to filter
-            current_messages = agent.messages
-
-            # Filter out messages belonging to the specific user, but keep:
-            # 1. System messages (role='system') - always keep
-            # 2. Messages from other users (user_id != specified user_id)
-            messages_to_keep = []
-            messages_to_remove = []
-
-            for message in current_messages:
-                if message.role == "system":
-                    # Always keep system messages
-                    messages_to_keep.append(message)
-                elif user_id is None or message.user_id == user_id:
-                    # Remove this user's messages (or all if user_id is None)
-                    messages_to_remove.append(message)
-                else:
-                    # Keep messages from other users
-                    messages_to_keep.append(message)
-
-            # Update the agent's messages relationship to only keep filtered messages
-            agent.messages = messages_to_keep
-
-            # Update message_ids to reflect the remaining messages
-            # Keep the order based on created_at timestamp
-            agent.message_ids = [msg.id for msg in messages_to_keep]
-
-            # Commit the update
-            await agent.update(db_session=session, actor=actor)
-
-            agent_state = agent.to_pydantic()
-
-        if add_default_initial_messages:
-            return await self.append_initial_message_sequence_to_in_context_messages(actor, agent_state, user_id=user_id)
-        else:
-            # We still want to always have a system message
-            init_messages = initialize_message_sequence(
-                agent_state=agent_state,
-                memory_edit_timestamp=get_utc_time(),
-                include_initial_boot_message=True,
-            )
-            system_message = PydanticMessage.dict_to_message(
-                agent_id=agent_state.id,
-                user_id=agent_state.created_by_id,
-                model=agent_state.llm_config.model,
-                openai_message_dict=init_messages[0],
+        if user_id:
+            await self.message_manager.hard_delete_user_messages_for_agent(
+                agent_id=agent_id,
+                user_id=user_id,
+                actor=actor,
+                keep_newest_n=0,
             )
-            return await self.append_to_in_context_messages([system_message], agent_id=agent_state.id, actor=actor)
+        else:
+            # Delete all non-system messages for every user of this agent
+            from sqlalchemy import delete
+
+            from mirix.orm.message import Message as MessageModel
+            from mirix.schemas.message import MessageRole
+
+            async with self.session_maker() as session:
+                await session.execute(
+                    delete(MessageModel).where(
+                        MessageModel.agent_id == agent_id,
+                        MessageModel.organization_id == actor.organization_id,
+                        MessageModel.role != MessageRole.system,
+                    )
+                )
+                await session.commit()
+
+        return await self.get_agent_by_id(agent_id=agent_id, actor=actor)
 
     # ======================================================================================================================
     # Tool Management
diff --git a/mirix/services/block_manager.py b/mirix/services/block_manager.py
index 1fc4ea51e..fe238ebb1 100755
--- a/mirix/services/block_manager.py
+++ b/mirix/services/block_manager.py
@@ -566,9 +566,10 @@ async def delete_by_user_id(self, user_id: str) -> int:
         Returns:
             Number of records deleted
         """
-        from mirix.database.redis_client import get_redis_client
         from sqlalchemy import delete
 
+        from mirix.database.redis_client import get_redis_client
+
         async with self.session_maker() as session:
             stmt = select(BlockModel.id).where(BlockModel.user_id == user_id)
             result = await session.execute(stmt)
diff --git a/mirix/services/client_manager.py b/mirix/services/client_manager.py
index ffcfecd47..00a5ebf0d 100644
--- a/mirix/services/client_manager.py
+++ b/mirix/services/client_manager.py
@@ -9,7 +9,6 @@
 from mirix.schemas.client import Client as PydanticClient
 from mirix.schemas.client import ClientUpdate
 from mirix.schemas.client_api_key import ClientApiKey as PydanticClientApiKey
-from mirix.schemas.client_api_key import ClientApiKeyCreate
 from mirix.security.api_keys import hash_api_key
 from mirix.services.organization_manager import OrganizationManager
 from mirix.utils import enforce_types
@@ -28,17 +27,13 @@ def __init__(self):
         self.session_maker = db_context
 
     @enforce_types
-    async def create_default_client(
-        self, org_id: str = OrganizationManager.DEFAULT_ORG_ID
-    ) -> PydanticClient:
+    async def create_default_client(self, org_id: str = OrganizationManager.DEFAULT_ORG_ID) -> PydanticClient:
         """Create the default client (async)."""
         async with self.session_maker() as session:
             try:
                 await OrganizationModel.read(db_session=session, identifier=org_id)
             except NoResultFound:
-                raise ValueError(
-                    f"No organization with {org_id} exists in the organization table."
-                ) from None
+                raise ValueError(f"No organization with {org_id} exists in the organization table.") from None
 
             try:
                 client = await ClientModel.read(db_session=session, identifier=self.DEFAULT_CLIENT_ID)
@@ -67,9 +62,7 @@ async def create_client(self, pydantic_client: PydanticClient) -> PydanticClient
     async def update_client(self, client_update: ClientUpdate) -> PydanticClient:
         """Update client details (with cache invalidation)."""
         async with self.session_maker() as session:
-            existing_client = await ClientModel.read(
-                db_session=session, identifier=client_update.id
-            )
+            existing_client = await ClientModel.read(db_session=session, identifier=client_update.id)
             update_data = client_update.model_dump(exclude_unset=True, exclude_none=True)
             for key, value in update_data.items():
                 setattr(existing_client, key, value)
@@ -133,9 +126,7 @@ async def get_client_by_api_key(self, api_key: str) -> Optional[PydanticClient]:
             if not api_key_record:
                 return None
 
-            client = await ClientModel.read(
-                db_session=session, identifier=api_key_record.client_id
-            )
+            client = await ClientModel.read(db_session=session, identifier=api_key_record.client_id)
             if client.is_deleted or client.status != "active":
                 return None
 
@@ -157,9 +148,7 @@ async def list_client_api_keys(self, client_id: str) -> List[PydanticClientApiKe
     async def revoke_client_api_key(self, api_key_id: str) -> PydanticClientApiKey:
         """Revoke an API key (set status to 'revoked')."""
         async with self.session_maker() as session:
-            api_key = await ClientApiKeyModel.read(
-                db_session=session, identifier=api_key_id
-            )
+            api_key = await ClientApiKeyModel.read(db_session=session, identifier=api_key_id)
             api_key.status = "revoked"
             await api_key.update(session, actor=None)
             return api_key.to_pydantic()
@@ -168,9 +157,7 @@ async def revoke_client_api_key(self, api_key_id: str) -> PydanticClientApiKey:
     async def delete_client_api_key(self, api_key_id: str) -> None:
         """Permanently delete an API key from the database."""
         async with self.session_maker() as session:
-            api_key = await ClientApiKeyModel.read(
-                db_session=session, identifier=api_key_id
-            )
+            api_key = await ClientApiKeyModel.read(db_session=session, identifier=api_key_id)
             session.delete(api_key)
             await session.commit()
 
@@ -178,9 +165,7 @@ async def delete_client_api_key(self, api_key_id: str) -> None:
     async def update_client_status(self, client_id: str, status: str) -> PydanticClient:
         """Update the status of a client (with cache invalidation)."""
         async with self.session_maker() as session:
-            existing_client = await ClientModel.read(
-                db_session=session, identifier=client_id
-            )
+            existing_client = await ClientModel.read(db_session=session, identifier=client_id)
             existing_client.status = status
             await existing_client.update_with_redis(session, actor=None)
             return existing_client.to_pydantic()
@@ -357,9 +342,7 @@ async def delete_client_by_id(self, client_id: str):
                     await redis_client.client.hset(client_key, "is_deleted", "true")
                     logger.debug("Updated client %s in cache (is_deleted=true)", client_id)
                 except Exception as e:
-                    logger.warning(
-                        "Failed to update client in Redis, removing instead: %s", e
-                    )
+                    logger.warning("Failed to update client in Redis, removing instead: %s", e)
                     await redis_client.delete(client_key)
 
                 for agent_id in agent_ids:
@@ -368,9 +351,7 @@ async def delete_client_by_id(self, client_id: str):
                         await redis_client.client.hset(agent_key, "is_deleted", "true")
                     except Exception:
                         await redis_client.delete(agent_key)
-                logger.debug(
-                    "Updated %d agents in Redis cache (is_deleted=true)", len(agent_ids)
-                )
+                logger.debug("Updated %d agents in Redis cache (is_deleted=true)", len(agent_ids))
 
                 logger.info(
                     "Client %s and all associated records soft deleted: "
@@ -385,9 +366,7 @@ async def delete_client_by_id(self, client_id: str):
                     message_count,
                 )
         except Exception as e:
-            logger.warning(
-                "Failed to update Redis cache for client %s: %s", client_id, e
-            )
+            logger.warning("Failed to update Redis cache for client %s: %s", client_id, e)
 
     async def delete_memories_by_client_id(self, client_id: str):
         """
@@ -471,9 +450,7 @@ async def delete_memories_by_client_id(self, client_id: str):
             async with self.session_maker() as session:
                 from mirix.orm.block import Block as BlockModel
 
-                stmt_ids = select(BlockModel.id).where(
-                    BlockModel._created_by_id == client_id
-                )
+                stmt_ids = select(BlockModel.id).where(BlockModel._created_by_id == client_id)
                 result_ids = await session.execute(stmt_ids)
                 block_ids = [row[0] for row in result_ids.all()]
 
@@ -485,9 +462,7 @@ async def delete_memories_by_client_id(self, client_id: str):
                     for block_id in block_ids:
                         await block_manager._invalidate_block_cache(block_id)
 
-                    stmt_del = delete(BlockModel).where(
-                        BlockModel._created_by_id == client_id
-                    )
+                    stmt_del = delete(BlockModel).where(BlockModel._created_by_id == client_id)
                     await session.execute(stmt_del)
                     await session.commit()
 
@@ -496,10 +471,7 @@ async def delete_memories_by_client_id(self, client_id: str):
 
                 redis_client = get_redis_client()
                 if redis_client:
-                    redis_keys = [
-                        f"{redis_client.BLOCK_PREFIX}{block_id}"
-                        for block_id in block_ids
-                    ]
+                    redis_keys = [f"{redis_client.BLOCK_PREFIX}{block_id}" for block_id in block_ids]
                     BATCH_SIZE = 1000
                     for i in range(0, len(redis_keys), BATCH_SIZE):
                         batch = redis_keys[i : i + BATCH_SIZE]
@@ -507,27 +479,15 @@ async def delete_memories_by_client_id(self, client_id: str):
 
             logger.debug("Bulk deleted %d blocks", block_count)
 
-            # Clear message_ids from agents in PostgreSQL (they reference deleted messages)
+            # Collect agent IDs for cache invalidation (messages already deleted above)
             agent_ids: List[str] = []
             async with self.session_maker() as session:
                 from mirix.orm.agent import Agent as AgentModel
 
-                stmt_agents = select(AgentModel).where(
-                    AgentModel._created_by_id == client_id
-                )
+                stmt_agents = select(AgentModel).where(AgentModel._created_by_id == client_id)
                 result_agents = await session.execute(stmt_agents)
                 agents = result_agents.scalars().all()
                 agent_ids = [agent.id for agent in agents]
-                for agent in agents:
-                    if agent.message_ids and len(agent.message_ids) > 0:
-                        agent.message_ids = [agent.message_ids[0]]
-
-                await session.commit()
-                logger.debug(
-                    "Cleared conversation message_ids from %d agents in PostgreSQL "
-                    "(kept system messages)",
-                    len(agent_ids),
-                )
 
             from mirix.database.cache_provider import get_cache_provider
 
@@ -591,14 +551,10 @@ async def get_client_by_id(self, client_id: str) -> PydanticClient:
 
                     cache_key = f"{cache_provider.CLIENT_PREFIX}{client_id}"
                     data = pydantic_client.model_dump(mode="json")
-                    await cache_provider.set_hash(
-                        cache_key, data, ttl=settings.redis_ttl_clients
-                    )
+                    await cache_provider.set_hash(cache_key, data, ttl=settings.redis_ttl_clients)
                     logger.debug("Populated cache for client %s", client_id)
             except Exception as e:
-                logger.warning(
-                    "Failed to populate cache for client %s: %s", client_id, e
-                )
+                logger.warning("Failed to populate cache for client %s: %s", client_id, e)
 
             return pydantic_client
 
@@ -612,9 +568,7 @@ async def get_default_client(self) -> PydanticClient:
 
             org_mgr = OrganizationManager()
             await org_mgr.get_default_organization()
-            return await self.create_default_client(
-                org_id=OrganizationManager.DEFAULT_ORG_ID
-            )
+            return await self.create_default_client(org_id=OrganizationManager.DEFAULT_ORG_ID)
 
     @enforce_types
     async def get_client_or_default(
@@ -659,7 +613,5 @@ async def list_clients(
     ) -> List[PydanticClient]:
         """List clients with pagination using cursor (id) and limit."""
         async with self.session_maker() as session:
-            results = await ClientModel.list(
-                db_session=session, cursor=cursor, limit=limit
-            )
+            results = await ClientModel.list(db_session=session, cursor=cursor, limit=limit)
             return [client.to_pydantic() for client in results]
diff --git a/mirix/services/cloud_file_mapping_manager.py b/mirix/services/cloud_file_mapping_manager.py
index 4b1f36550..d8af9298d 100644
--- a/mirix/services/cloud_file_mapping_manager.py
+++ b/mirix/services/cloud_file_mapping_manager.py
@@ -14,38 +14,28 @@ def __init__(self):
 
         self.session_maker = db_context
 
-    async def add_mapping(
-        self, cloud_file_id, local_file_id, timestamp, force_add=False
-    ):
+    async def add_mapping(self, cloud_file_id, local_file_id, timestamp, force_add=False):
         """Add a mapping from a cloud file to a local file."""
         async with self.session_maker() as session:
             try:
-                existing = await CloudFileMapping.read(
-                    db_session=session, cloud_file_id=cloud_file_id
-                )
+                existing = await CloudFileMapping.read(db_session=session, cloud_file_id=cloud_file_id)
             except Exception:
                 existing = None
             if existing:
                 if force_add:
                     await existing.hard_delete(session)
                 else:
-                    raise ValueError(
-                        f"Mapping already exists for cloud file {cloud_file_id}"
-                    )
+                    raise ValueError(f"Mapping already exists for cloud file {cloud_file_id}")
 
             try:
-                existing = await CloudFileMapping.read(
-                    db_session=session, local_file_id=local_file_id
-                )
+                existing = await CloudFileMapping.read(db_session=session, local_file_id=local_file_id)
             except Exception:
                 existing = None
             if existing:
                 if force_add:
                     await existing.hard_delete(session)
                 else:
-                    raise ValueError(
-                        f"Mapping already exists for local file {local_file_id}"
-                    )
+                    raise ValueError(f"Mapping already exists for local file {local_file_id}")
 
             pydantic_mapping_dict = {
                 "cloud_file_id": cloud_file_id,
@@ -56,9 +46,7 @@ async def add_mapping(
             }
             from mirix.services.organization_manager import OrganizationManager
 
-            pydantic_mapping_dict["organization_id"] = (
-                OrganizationManager.DEFAULT_ORG_ID
-            )
+            pydantic_mapping_dict["organization_id"] = OrganizationManager.DEFAULT_ORG_ID
 
             mapping = CloudFileMapping(**pydantic_mapping_dict)
             await mapping.create(session)
@@ -68,9 +56,7 @@ async def get_local_file(self, cloud_file_id):
         """Get the local file ID for a cloud file."""
         async with self.session_maker() as session:
             try:
-                mapping = await CloudFileMapping.read(
-                    db_session=session, cloud_file_id=cloud_file_id
-                )
+                mapping = await CloudFileMapping.read(db_session=session, cloud_file_id=cloud_file_id)
                 return mapping.local_file_id if mapping else None
             except Exception:
                 return None
@@ -79,76 +65,56 @@ async def get_cloud_file(self, local_file_id):
         """Get the cloud file ID for a local file."""
         async with self.session_maker() as session:
             try:
-                mapping = await CloudFileMapping.read(
-                    db_session=session, local_file_id=local_file_id
-                )
+                mapping = await CloudFileMapping.read(db_session=session, local_file_id=local_file_id)
                 return mapping.cloud_file_id if mapping else None
             except Exception:
                 return None
 
-    async def delete_mapping(
-        self, cloud_file_id=None, local_file_id=None
-    ) -> None:
+    async def delete_mapping(self, cloud_file_id=None, local_file_id=None) -> None:
         """Delete a mapping."""
         async with self.session_maker() as session:
             if cloud_file_id is not None:
                 try:
-                    mapping = await CloudFileMapping.read(
-                        db_session=session, cloud_file_id=cloud_file_id
-                    )
+                    mapping = await CloudFileMapping.read(db_session=session, cloud_file_id=cloud_file_id)
                     await mapping.hard_delete(session)
                 except Exception:
                     pass
             if local_file_id is not None:
                 try:
-                    mapping = await CloudFileMapping.read(
-                        db_session=session, local_file_id=local_file_id
-                    )
+                    mapping = await CloudFileMapping.read(db_session=session, local_file_id=local_file_id)
                     await mapping.hard_delete(session)
                 except Exception:
                     pass
 
-    async def check_if_existing(
-        self, cloud_file_id=None, local_file_id=None
-    ) -> bool:
+    async def check_if_existing(self, cloud_file_id=None, local_file_id=None) -> bool:
         """Check if the file_ids exist in the database."""
         async with self.session_maker() as session:
             if cloud_file_id is not None:
                 try:
-                    await CloudFileMapping.read(
-                        db_session=session, cloud_file_id=cloud_file_id
-                    )
+                    await CloudFileMapping.read(db_session=session, cloud_file_id=cloud_file_id)
                     return True
                 except Exception:
                     pass
             elif local_file_id is not None:
                 try:
-                    await CloudFileMapping.read(
-                        db_session=session, local_file_id=local_file_id
-                    )
+                    await CloudFileMapping.read(db_session=session, local_file_id=local_file_id)
                     return True
                 except Exception:
                     pass
         return False
 
-    async def set_processed(
-        self, cloud_file_id=None, local_file_id=None
-    ) -> PydanticCloudFileMapping:
+    async def set_processed(self, cloud_file_id=None, local_file_id=None) -> PydanticCloudFileMapping:
         """Set status to processed."""
         async with self.session_maker() as session:
             mapping = None
             if cloud_file_id is not None:
                 try:
-                    mapping = await CloudFileMapping.read(
-                        db_session=session, cloud_file_id=cloud_file_id
-                    )
+                    mapping = await CloudFileMapping.read(db_session=session, cloud_file_id=cloud_file_id)
                 except Exception:
                     pass
             elif local_file_id is not None:
                 try:
-                    mapping = await CloudFileMapping.read(
-                        db_session=session, local_file_id=local_file_id
-                    )
+                    mapping = await CloudFileMapping.read(db_session=session, local_file_id=local_file_id)
                 except Exception:
                     pass
             if mapping is None:
diff --git a/mirix/services/episodic_memory_manager.py b/mirix/services/episodic_memory_manager.py
index 68ef38cb2..ca5da4be9 100755
--- a/mirix/services/episodic_memory_manager.py
+++ b/mirix/services/episodic_memory_manager.py
@@ -24,6 +24,11 @@
 
 logger = get_logger(__name__)
 
+# Diagnostic flag for MissingGreenlet debugging
+import os
+
+_TRACE_MISSING_GREENLET = os.getenv("MIRIX_TRACE_MISSING_GREENLET", "false").lower() == "true"
+
 
 class EpisodicMemoryManager:
     """Manager class to handle business logic related to Episodic episodic_memory items."""
@@ -260,9 +265,7 @@ async def create_episodic_memory(
         if not episodic_memory.id:
             from mirix.utils import generate_unique_short_id_async
 
-            episodic_memory.id = await generate_unique_short_id_async(
-                self.session_maker, EpisodicEvent, "ep"
-            )
+            episodic_memory.id = await generate_unique_short_id_async(self.session_maker, EpisodicEvent, "ep")
 
         # Convert the Pydantic model into a dict
         episodic_memory_dict = episodic_memory.model_dump()
@@ -349,9 +352,7 @@ async def delete_by_client_id(self, actor: PydanticClient) -> int:
 
         async with self.session_maker() as session:
             # Get IDs for Redis cleanup (only fetch IDs, not full objects)
-            result = await session.execute(
-                select(EpisodicEvent.id).where(EpisodicEvent.client_id == actor.id)
-            )
+            result = await session.execute(select(EpisodicEvent.id).where(EpisodicEvent.client_id == actor.id))
             item_ids = [row[0] for row in result.all()]
 
             count = len(item_ids)
@@ -359,9 +360,7 @@ async def delete_by_client_id(self, actor: PydanticClient) -> int:
                 return 0
 
             # Bulk delete in single query
-            await session.execute(
-                delete(EpisodicEvent).where(EpisodicEvent.client_id == actor.id)
-            )
+            await session.execute(delete(EpisodicEvent).where(EpisodicEvent.client_id == actor.id))
 
             await session.commit()
 
@@ -498,18 +497,14 @@ async def delete_by_user_id(self, user_id: str) -> int:
         from mirix.database.redis_client import get_redis_client
 
         async with self.session_maker() as session:
-            result = await session.execute(
-                select(EpisodicEvent.id).where(EpisodicEvent.user_id == user_id)
-            )
+            result = await session.execute(select(EpisodicEvent.id).where(EpisodicEvent.user_id == user_id))
             item_ids = [row[0] for row in result.all()]
 
             count = len(item_ids)
             if count == 0:
                 return 0
 
-            await session.execute(
-                delete(EpisodicEvent).where(EpisodicEvent.user_id == user_id)
-            )
+            await session.execute(delete(EpisodicEvent).where(EpisodicEvent.user_id == user_id))
 
             await session.commit()
 
@@ -741,7 +736,9 @@ async def list_episodic_memory(
                         from mirix.constants import MAX_EMBEDDING_DIM
                         from mirix.embeddings import embedding_model
 
-                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(query)
+                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(
+                            query
+                        )
                         embedded_text = np.array(embedded_text)
                         embedded_text = np.pad(
                             embedded_text,
@@ -1458,7 +1455,9 @@ async def list_episodic_memory_by_org(
                         from mirix.constants import MAX_EMBEDDING_DIM
                         from mirix.embeddings import embedding_model
 
-                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(query)
+                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(
+                            query
+                        )
                         embedded_text = np.array(embedded_text)
                         embedded_text = np.pad(
                             embedded_text,
@@ -1543,7 +1542,30 @@ async def list_episodic_memory_by_org(
                     base_query = base_query.limit(limit)
                 result = await session.execute(base_query)
                 episodic_memory = result.scalars().all()
-                return [event.to_pydantic() for event in episodic_memory]
+
+                if _TRACE_MISSING_GREENLET:
+                    logger.info(
+                        "Converting %d episodic events to Pydantic in list_episodic_memory_by_org", len(episodic_memory)
+                    )
+                    pydantic_events = []
+                    for i, event in enumerate(episodic_memory):
+                        try:
+                            pydantic_events.append(event.to_pydantic())
+                        except Exception as e:
+                            if "MissingGreenlet" in str(type(e).__name__) or "greenlet" in str(e).lower():
+                                import traceback
+
+                                logger.error(
+                                    "MissingGreenlet in list_episodic_memory_by_org at index %d, event_id=%s\n"
+                                    "Full traceback:\n%s",
+                                    i,
+                                    event.id,
+                                    traceback.format_exc(),
+                                )
+                            raise
+                    return pydantic_events
+                else:
+                    return [event.to_pydantic() for event in episodic_memory]
 
             if search_method == "embedding":
                 embed_query = True
@@ -1583,7 +1605,7 @@ async def list_episodic_memory_by_org(
                 base_query = base_query.order_by(embedding_query_field)
             elif search_method == "bm25":
                 # Use PostgreSQL native full-text search if available
-                from sqlalchemy import func, text
+                from sqlalchemy import func
 
                 # Determine search field
                 if not search_field or search_field == "details":
diff --git a/mirix/services/file_manager.py b/mirix/services/file_manager.py
index c63ce1b29..8157fa2a8 100644
--- a/mirix/services/file_manager.py
+++ b/mirix/services/file_manager.py
@@ -19,9 +19,7 @@ def __init__(self):
         self.session_maker = db_context
 
     @enforce_types
-    async def create_file_metadata(
-        self, pydantic_file: PydanticFileMetadata
-    ) -> PydanticFileMetadata:
+    async def create_file_metadata(self, pydantic_file: PydanticFileMetadata) -> PydanticFileMetadata:
         """Create new file metadata."""
         async with self.session_maker() as session:
             file_metadata = FileMetadataModel(**pydantic_file.model_dump())
@@ -32,9 +30,7 @@ async def create_file_metadata(
     async def get_file_metadata_by_id(self, file_id: str) -> PydanticFileMetadata:
         """Get file metadata by ID."""
         async with self.session_maker() as session:
-            file_metadata = await FileMetadataModel.read(
-                db_session=session, identifier=file_id
-            )
+            file_metadata = await FileMetadataModel.read(db_session=session, identifier=file_id)
             return file_metadata.to_pydantic()
 
     @enforce_types
@@ -55,14 +51,10 @@ async def get_files_by_organization_id(
             return [f.to_pydantic() for f in results]
 
     @enforce_types
-    async def update_file_metadata(
-        self, file_id: str, **kwargs
-    ) -> PydanticFileMetadata:
+    async def update_file_metadata(self, file_id: str, **kwargs) -> PydanticFileMetadata:
         """Update file metadata."""
         async with self.session_maker() as session:
-            file_metadata = await FileMetadataModel.read(
-                db_session=session, identifier=file_id
-            )
+            file_metadata = await FileMetadataModel.read(db_session=session, identifier=file_id)
             for key, value in kwargs.items():
                 if hasattr(file_metadata, key) and value is not None:
                     setattr(file_metadata, key, value)
@@ -74,20 +66,14 @@ async def update_file_metadata(
     async def delete_file_metadata(self, file_id: str) -> None:
         """Delete file metadata by ID."""
         async with self.session_maker() as session:
-            file_metadata = await FileMetadataModel.read(
-                db_session=session, identifier=file_id
-            )
+            file_metadata = await FileMetadataModel.read(db_session=session, identifier=file_id)
             await file_metadata.hard_delete(session)
 
     @enforce_types
-    async def list_files(
-        self, cursor: Optional[str] = None, limit: Optional[int] = 50
-    ) -> List[PydanticFileMetadata]:
+    async def list_files(self, cursor: Optional[str] = None, limit: Optional[int] = 50) -> List[PydanticFileMetadata]:
         """List all files with pagination."""
         async with self.session_maker() as session:
-            results = await FileMetadataModel.list(
-                db_session=session, cursor=cursor, limit=limit
-            )
+            results = await FileMetadataModel.list(db_session=session, cursor=cursor, limit=limit)
             return [f.to_pydantic() for f in results]
 
     @enforce_types
@@ -140,14 +126,10 @@ async def search_files_by_name(
         """Search files by name pattern."""
         async with self.session_maker() as session:
             stmt = select(FileMetadataModel).where(
-                func.lower(FileMetadataModel.file_name).contains(
-                    func.lower(file_name)
-                )
+                func.lower(FileMetadataModel.file_name).contains(func.lower(file_name))
             )
             if organization_id:
-                stmt = stmt.where(
-                    FileMetadataModel.organization_id == organization_id
-                )
+                stmt = stmt.where(FileMetadataModel.organization_id == organization_id)
             result = await session.execute(stmt)
             rows = result.scalars().all()
             return [f.to_pydantic() for f in rows]
@@ -158,53 +140,37 @@ async def get_files_by_type(
     ) -> List[PydanticFileMetadata]:
         """Get files by file type."""
         async with self.session_maker() as session:
-            stmt = select(FileMetadataModel).where(
-                FileMetadataModel.file_type == file_type
-            )
+            stmt = select(FileMetadataModel).where(FileMetadataModel.file_type == file_type)
             if organization_id:
-                stmt = stmt.where(
-                    FileMetadataModel.organization_id == organization_id
-                )
+                stmt = stmt.where(FileMetadataModel.organization_id == organization_id)
             result = await session.execute(stmt)
             rows = result.scalars().all()
             return [f.to_pydantic() for f in rows]
 
     @enforce_types
-    async def check_file_exists(
-        self, file_path: str, organization_id: Optional[str] = None
-    ) -> bool:
+    async def check_file_exists(self, file_path: str, organization_id: Optional[str] = None) -> bool:
         """Check if a file with the given path exists in the database."""
         async with self.session_maker() as session:
             try:
-                stmt = select(FileMetadataModel).where(
-                    FileMetadataModel.file_path == file_path
-                )
+                stmt = select(FileMetadataModel).where(FileMetadataModel.file_path == file_path)
                 if organization_id:
-                    stmt = stmt.where(
-                        FileMetadataModel.organization_id == organization_id
-                    )
+                    stmt = stmt.where(FileMetadataModel.organization_id == organization_id)
                 result = await session.execute(stmt)
                 return result.scalar_one_or_none() is not None
             except Exception:
                 return False
 
     @enforce_types
-    async def get_file_stats(
-        self, organization_id: Optional[str] = None
-    ) -> dict:
+    async def get_file_stats(self, organization_id: Optional[str] = None) -> dict:
         """Get file statistics for an organization or globally."""
         async with self.session_maker() as session:
             stmt = select(
                 func.count(FileMetadataModel.id).label("total_files"),
                 func.sum(FileMetadataModel.file_size).label("total_size"),
-                func.count(func.distinct(FileMetadataModel.file_type)).label(
-                    "unique_types"
-                ),
+                func.count(func.distinct(FileMetadataModel.file_type)).label("unique_types"),
             )
             if organization_id:
-                stmt = stmt.where(
-                    FileMetadataModel.organization_id == organization_id
-                )
+                stmt = stmt.where(FileMetadataModel.organization_id == organization_id)
             result = await session.execute(stmt)
             row = result.one()
             return {
diff --git a/mirix/services/helpers/agent_manager_helper.py b/mirix/services/helpers/agent_manager_helper.py
index 8bb05d2f7..ad104c986 100755
--- a/mirix/services/helpers/agent_manager_helper.py
+++ b/mirix/services/helpers/agent_manager_helper.py
@@ -3,19 +3,14 @@
 
 from sqlalchemy import select
 
-from mirix import system
 from mirix.constants import IN_CONTEXT_MEMORY_KEYWORD, STRUCTURED_OUTPUT_MODELS
 from mirix.helpers import ToolRulesSolver
 from mirix.orm.agent import Agent as AgentModel
 from mirix.orm.errors import NoResultFound
 from mirix.prompts import gpt_system
-from mirix.schemas.agent import AgentState, AgentType
-from mirix.schemas.client import Client
-from mirix.schemas.enums import MessageRole
+from mirix.schemas.agent import AgentType
 from mirix.schemas.memory import Memory
-from mirix.schemas.message import Message, MessageCreate
 from mirix.schemas.tool_rule import ToolRule
-from mirix.schemas.user import User
 from mirix.utils import get_local_time
 
 
@@ -49,9 +44,7 @@ async def _process_relationship(
             setattr(agent, relationship_name, [])
         return
 
-    result = await session.execute(
-        select(model_class).where(model_class.id.in_(item_ids))
-    )
+    result = await session.execute(select(model_class).where(model_class.id.in_(item_ids)))
     found_items = result.scalars().all()
 
     if not allow_partial and len(found_items) != len(item_ids):
@@ -179,67 +172,6 @@ def compile_system_message(
     return formatted_prompt
 
 
-def initialize_message_sequence(
-    agent_state: AgentState,
-    memory_edit_timestamp: Optional[datetime.datetime] = None,
-    include_initial_boot_message: bool = True,
-    previous_message_count: int = 0,
-    archival_memory_size: int = 0,
-) -> List[dict]:
-    if memory_edit_timestamp is None:
-        memory_edit_timestamp = get_local_time()
-
-    messages = [
-        {"role": "system", "content": agent_state.system},
-    ]
-
-    return messages
-
-
-def package_initial_message_sequence(
-    agent_id: str,
-    initial_message_sequence: List[MessageCreate],
-    model: str,
-    actor: Client,
-    user_id: Optional[str] = None,
-) -> List[Message]:
-    """
-    Package initial messages for an agent.
-
-    Args:
-        agent_id: The agent ID these messages belong to.
-        initial_message_sequence: List of messages to package.
-        model: The LLM model name.
-        actor: The Client performing the operation (used for organization_id).
-        user_id: The user ID to associate with these messages. If not provided,
-                 messages will have user_id=None.
-    """
-    init_messages = []
-    for message_create in initial_message_sequence:
-        if message_create.role == MessageRole.user:
-            packed_message = system.package_user_message(
-                user_message=message_create.text,
-            )
-        elif message_create.role == MessageRole.system:
-            packed_message = system.package_system_message(
-                system_message=message_create.text,
-            )
-        else:
-            raise ValueError(f"Invalid message role: {message_create.role}")
-
-        init_messages.append(
-            Message(
-                role=message_create.role,
-                text=packed_message,
-                organization_id=actor.organization_id,
-                user_id=user_id,
-                agent_id=agent_id,
-                model=model,
-            )
-        )
-    return init_messages
-
-
 def check_supports_structured_output(model: str, tool_rules: List[ToolRule]) -> bool:
     if model not in STRUCTURED_OUTPUT_MODELS:
         if len(ToolRulesSolver(tool_rules=tool_rules).init_tool_rules) > 1:
diff --git a/mirix/services/knowledge_vault_manager.py b/mirix/services/knowledge_vault_manager.py
index 7fac83181..12f29634b 100755
--- a/mirix/services/knowledge_vault_manager.py
+++ b/mirix/services/knowledge_vault_manager.py
@@ -440,7 +440,9 @@ async def get_item_by_id(
                     id="system-default-client", organization_id=user.organization_id, name="system-client"
                 )
 
-                item = await KnowledgeVaultItem.read(db_session=session, identifier=knowledge_vault_item_id, actor=actor)
+                item = await KnowledgeVaultItem.read(
+                    db_session=session, identifier=knowledge_vault_item_id, actor=actor
+                )
                 pydantic_item = item.to_pydantic()
 
                 try:
@@ -506,9 +508,7 @@ async def create_item(
         if not knowledge_vault_item.id:
             from mirix.utils import generate_unique_short_id_async
 
-            knowledge_vault_item.id = await generate_unique_short_id_async(
-                self.session_maker, KnowledgeVaultItem, "kv"
-            )
+            knowledge_vault_item.id = await generate_unique_short_id_async(self.session_maker, KnowledgeVaultItem, "kv")
 
         item_data = knowledge_vault_item.model_dump()
 
@@ -950,7 +950,9 @@ async def delete_knowledge_by_id(self, knowledge_vault_item_id: str, actor: Pyda
         """Delete a knowledge vault item by ID (removes from cache)."""
         async with self.session_maker() as session:
             try:
-                item = await KnowledgeVaultItem.read(db_session=session, identifier=knowledge_vault_item_id, actor=actor)
+                item = await KnowledgeVaultItem.read(
+                    db_session=session, identifier=knowledge_vault_item_id, actor=actor
+                )
                 # Remove from cache
                 from mirix.database.cache_provider import get_cache_provider
 
@@ -1114,9 +1116,7 @@ async def delete_by_user_id(self, user_id: str) -> int:
 
         async with self.session_maker() as session:
             # Get IDs for Redis cleanup (only fetch IDs, not full objects)
-            result = await session.execute(
-                select(KnowledgeVaultItem.id).where(KnowledgeVaultItem.user_id == user_id)
-            )
+            result = await session.execute(select(KnowledgeVaultItem.id).where(KnowledgeVaultItem.user_id == user_id))
             item_ids = [row[0] for row in result.all()]
 
             count = len(item_ids)
@@ -1184,7 +1184,9 @@ async def list_knowledge_by_org(
                         from mirix.constants import MAX_EMBEDDING_DIM
                         from mirix.embeddings import embedding_model
 
-                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(query)
+                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(
+                            query
+                        )
                         embedded_text = np.array(embedded_text)
                         embedded_text = np.pad(
                             embedded_text,
diff --git a/mirix/services/mcp_tool_registry.py b/mirix/services/mcp_tool_registry.py
index 33dc94354..3850047ca 100644
--- a/mirix/services/mcp_tool_registry.py
+++ b/mirix/services/mcp_tool_registry.py
@@ -202,9 +202,7 @@ def _json_type_to_python_type(self, json_type: str) -> str:
         }
         return type_map.get(json_type, "str")
 
-    async def unregister_mcp_tools(
-        self, actor: PydanticClient, server_name: Optional[str] = None
-    ) -> int:
+    async def unregister_mcp_tools(self, actor: PydanticClient, server_name: Optional[str] = None) -> int:
         """
         Unregister MCP tools from database.
 
@@ -245,9 +243,7 @@ async def sync_mcp_tools(self, actor: PydanticClient) -> Dict[str, int]:
             current_tool_names.update(t["full_name"] for t in tools)
 
         existing_tools = await self.tool_manager.list_tools(actor)
-        existing_mcp_tools = [
-            t for t in existing_tools if t.tool_type == ToolType.MIRIX_MCP
-        ]
+        existing_mcp_tools = [t for t in existing_tools if t.tool_type == ToolType.MIRIX_MCP]
         existing_tool_names = {t.name for t in existing_mcp_tools}
 
         new_tools = current_tool_names - existing_tool_names
@@ -255,9 +251,7 @@ async def sync_mcp_tools(self, actor: PydanticClient) -> Dict[str, int]:
         if new_tools:
             filtered_discovered = {}
             for sname, tools in discovered_tools.items():
-                filtered_tools = [
-                    t for t in tools if t["full_name"] in new_tools
-                ]
+                filtered_tools = [t for t in tools if t["full_name"] in new_tools]
                 if filtered_tools:
                     filtered_discovered[sname] = filtered_tools
             old_cache = self._mcp_tool_cache
diff --git a/mirix/services/message_manager.py b/mirix/services/message_manager.py
index 1ccffdb3d..ca0a4b5e5 100755
--- a/mirix/services/message_manager.py
+++ b/mirix/services/message_manager.py
@@ -135,10 +135,7 @@ async def create_many_messages(
         user_id: Optional[str] = None,
     ) -> List[PydanticMessage]:
         """Create multiple messages."""
-        return [
-            await self.create_message(m, actor=actor, client_id=client_id, user_id=user_id)
-            for m in pydantic_msgs
-        ]
+        return [await self.create_message(m, actor=actor, client_id=client_id, user_id=user_id) for m in pydantic_msgs]
 
     @enforce_types
     async def update_message_by_id(
@@ -358,9 +355,10 @@ async def delete_by_user_id(self, user_id: str) -> int:
         Returns:
             Number of records deleted
         """
+        from sqlalchemy import delete
+
         from mirix.database.redis_client import get_redis_client
         from mirix.schemas.message import MessageRole
-        from sqlalchemy import delete
 
         async with self.session_maker() as session:
             # Get IDs for non-system messages only (preserve system messages)
@@ -515,114 +513,127 @@ async def list_messages_for_agent(
 
             return [msg.to_pydantic() for msg in results]
 
-    @enforce_types
-    async def delete_detached_messages_for_agent(self, agent_id: str, actor: PydanticClient) -> int:
+    async def get_messages_for_agent_user(
+        self,
+        agent_id: str,
+        user_id: str,
+        actor: PydanticClient,
+        limit: int = 10,
+    ) -> List[PydanticMessage]:
         """
-        Delete messages that belong to an agent but are not in the agent's current message_ids list.
+        Fetch the most recent N messages for a given (agent, user) pair, returned in
+        chronological order (oldest first).
 
-        This is useful for cleaning up messages that were removed from context during
-        context window management but still exist in the database.
+        Uses the composite index ix_messages_agent_user_created_at for efficient retrieval.
 
         Args:
-            agent_id: The ID of the agent to clean up messages for
-            actor: The user performing this action
+            agent_id: The agent whose messages to retrieve
+            user_id: The user whose messages to retrieve
+            actor: Client performing the operation (for org scoping)
+            limit: Maximum number of messages to return (newest N, then reversed)
 
         Returns:
-            int: Number of messages deleted
+            List of messages in chronological order
         """
-        async with self.session_maker() as session:
-            # First, get the agent to access its current message_ids
-            from mirix.orm.agent import Agent as AgentModel
+        from sqlalchemy import desc
 
-            try:
-                agent = await AgentModel.read(db_session=session, identifier=agent_id, actor=actor)
-            except NoResultFound:
-                raise ValueError(f"Agent with id {agent_id} not found.")
-
-            # Get current message_ids (messages that should be kept)
-            current_message_ids = set(agent.message_ids or [])
-
-            # Find all messages for this agent
-            all_messages = await MessageModel.list(
-                db_session=session,
-                agent_id=agent_id,
-                organization_id=actor.organization_id,
-                limit=None,  # Get all messages
+        async with self.session_maker() as session:
+            stmt = (
+                select(MessageModel)
+                .where(
+                    MessageModel.agent_id == agent_id,
+                    MessageModel.user_id == user_id,
+                    MessageModel.organization_id == actor.organization_id,
+                    MessageModel.is_deleted == False,
+                )
+                .order_by(desc(MessageModel.created_at), desc(MessageModel.id))
+                .limit(limit)
             )
+            result = await session.execute(stmt)
+            messages = result.scalars().all()
 
-            # Identify detached messages (not in current message_ids)
-            detached_messages = [msg for msg in all_messages if msg.id not in current_message_ids]
-
-            # Delete detached messages (and clean up Redis cache)
-            deleted_count = 0
-            from mirix.database.redis_client import get_redis_client
-
-            redis_client = get_redis_client()
-
-            for msg in detached_messages:
-                # Remove from Redis cache
-                if redis_client:
-                    redis_key = f"{redis_client.MESSAGE_PREFIX}{msg.id}"
-                    await redis_client.delete(redis_key)
-                await msg.hard_delete(session, actor=actor)
-                deleted_count += 1
-
-            await session.commit()
-            return deleted_count
+        # Reverse to chronological order
+        return [msg.to_pydantic() for msg in reversed(messages)]
 
-    @enforce_types
-    async def cleanup_all_detached_messages(self, actor: PydanticClient) -> Dict[str, int]:
+    async def hard_delete_user_messages_for_agent(
+        self,
+        agent_id: str,
+        user_id: str,
+        actor: PydanticClient,
+        keep_newest_n: int = 0,
+    ) -> int:
         """
-        Cleanup detached messages for all agents in the organization.
+        Hard-delete messages for a (agent, user) pair, optionally keeping the newest N.
+
+        Deletes from both the database and Redis cache.
 
         Args:
-            actor: The user performing this action
+            agent_id: The agent whose messages to prune
+            user_id: The user whose messages to prune
+            actor: Client performing the operation (for org scoping)
+            keep_newest_n: How many of the most-recent messages to retain. 0 = delete all.
 
         Returns:
-            Dict[str, int]: Dictionary mapping agent_id to number of messages deleted
+            Number of messages deleted
         """
-        from mirix.orm.agent import Agent as AgentModel
-
-        async with self.session_maker() as session:
-            # Get all agents for this organization
-            agents = await AgentModel.list(
-                db_session=session, organization_id=actor.organization_id, limit=None
-            )
+        from sqlalchemy import delete, desc
 
-            cleanup_results = {}
-            total_deleted = 0
-
-            for agent in agents:
-                # Get current message_ids for this agent
-                current_message_ids = set(agent.message_ids or [])
+        from mirix.database.redis_client import get_redis_client
 
-                # Find all messages for this agent
-                all_messages = await MessageModel.list(
-                    db_session=session,
-                    agent_id=agent.id,
-                    organization_id=actor.organization_id,
-                    limit=None,
+        async with self.session_maker() as session:
+            # Identify IDs to keep (the newest N)
+            keep_ids: set = set()
+            if keep_newest_n > 0:
+                keep_stmt = (
+                    select(MessageModel.id)
+                    .where(
+                        MessageModel.agent_id == agent_id,
+                        MessageModel.user_id == user_id,
+                        MessageModel.organization_id == actor.organization_id,
+                        MessageModel.is_deleted == False,
+                    )
+                    .order_by(desc(MessageModel.created_at), desc(MessageModel.id))
+                    .limit(keep_newest_n)
                 )
+                keep_result = await session.execute(keep_stmt)
+                keep_ids = {row[0] for row in keep_result.all()}
 
-                # Identify and delete detached messages
-                detached_messages = [msg for msg in all_messages if msg.id not in current_message_ids]
-
-                deleted_count = 0
-                from mirix.database.redis_client import get_redis_client
+            # Collect IDs that will be deleted (for cache invalidation)
+            select_stmt = select(MessageModel.id).where(
+                MessageModel.agent_id == agent_id,
+                MessageModel.user_id == user_id,
+                MessageModel.organization_id == actor.organization_id,
+                MessageModel.is_deleted == False,
+            )
+            if keep_ids:
+                select_stmt = select_stmt.where(MessageModel.id.not_in(keep_ids))
 
-                redis_client = get_redis_client()
+            id_result = await session.execute(select_stmt)
+            delete_ids = [row[0] for row in id_result.all()]
 
-                for msg in detached_messages:
-                    # Remove from Redis cache
-                    if redis_client:
-                        redis_key = f"{redis_client.MESSAGE_PREFIX}{msg.id}"
-                        await redis_client.delete(redis_key)
-                    await msg.hard_delete(session)
-                    deleted_count += 1
+            count = len(delete_ids)
+            if count == 0:
+                return 0
 
-                cleanup_results[agent.id] = deleted_count
-                total_deleted += deleted_count
+            # Bulk delete
+            del_stmt = delete(MessageModel).where(
+                MessageModel.agent_id == agent_id,
+                MessageModel.user_id == user_id,
+                MessageModel.organization_id == actor.organization_id,
+                MessageModel.is_deleted == False,
+            )
+            if keep_ids:
+                del_stmt = del_stmt.where(MessageModel.id.not_in(keep_ids))
 
+            await session.execute(del_stmt)
             await session.commit()
-            cleanup_results["total"] = total_deleted
-            return cleanup_results
+
+        # Evict from Redis cache
+        redis_client = get_redis_client()
+        if redis_client and delete_ids:
+            BATCH_SIZE = 1000
+            for i in range(0, len(delete_ids), BATCH_SIZE):
+                batch = [f"{redis_client.MESSAGE_PREFIX}{mid}" for mid in delete_ids[i : i + BATCH_SIZE]]
+                await redis_client.client.delete(*batch)
+
+        return count
diff --git a/mirix/services/organization_manager.py b/mirix/services/organization_manager.py
index 24dddc318..3ecb69527 100755
--- a/mirix/services/organization_manager.py
+++ b/mirix/services/organization_manager.py
@@ -86,14 +86,10 @@ async def _create_organization(self, pydantic_org: PydanticOrganization) -> Pyda
     @enforce_types
     async def create_default_organization(self) -> PydanticOrganization:
         """Create the default organization."""
-        return await self.create_organization(
-            PydanticOrganization(name=self.DEFAULT_ORG_NAME, id=self.DEFAULT_ORG_ID)
-        )
+        return await self.create_organization(PydanticOrganization(name=self.DEFAULT_ORG_NAME, id=self.DEFAULT_ORG_ID))
 
     @enforce_types
-    async def update_organization_name_using_id(
-        self, org_id: str, name: Optional[str] = None
-    ) -> PydanticOrganization:
+    async def update_organization_name_using_id(self, org_id: str, name: Optional[str] = None) -> PydanticOrganization:
         """Update an organization (with cache invalidation)."""
         async with self.session_maker() as session:
             org = await OrganizationModel.read(db_session=session, identifier=org_id)
diff --git a/mirix/services/procedural_memory_manager.py b/mirix/services/procedural_memory_manager.py
index cda827658..d2c589706 100755
--- a/mirix/services/procedural_memory_manager.py
+++ b/mirix/services/procedural_memory_manager.py
@@ -495,9 +495,7 @@ async def create_item(
         if not item_data.id:
             from mirix.utils import generate_unique_short_id_async
 
-            item_data.id = await generate_unique_short_id_async(
-                self.session_maker, ProceduralMemoryItem, "proc"
-            )
+            item_data.id = await generate_unique_short_id_async(self.session_maker, ProceduralMemoryItem, "proc")
 
         data_dict = item_data.model_dump()
 
@@ -708,9 +706,7 @@ async def list_procedures(
 
                 from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-                query_stmt = apply_filter_tags_sqlalchemy(
-                    query_stmt, ProceduralMemoryItem, filter_tags, scopes=scopes
-                )
+                query_stmt = apply_filter_tags_sqlalchemy(query_stmt, ProceduralMemoryItem, filter_tags, scopes=scopes)
 
                 if limit:
                     query_stmt = query_stmt.limit(limit)
@@ -740,9 +736,7 @@ async def list_procedures(
 
                 from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-                base_query = apply_filter_tags_sqlalchemy(
-                    base_query, ProceduralMemoryItem, filter_tags, scopes=scopes
-                )
+                base_query = apply_filter_tags_sqlalchemy(base_query, ProceduralMemoryItem, filter_tags, scopes=scopes)
 
                 if search_method == "embedding":
                     main_query = await build_query(
@@ -1199,7 +1193,9 @@ async def list_procedures_by_org(
                         from mirix.constants import MAX_EMBEDDING_DIM
                         from mirix.embeddings import embedding_model
 
-                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(query)
+                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(
+                            query
+                        )
                         embedded_text = np.array(embedded_text)
                         embedded_text = np.pad(
                             embedded_text,
@@ -1245,9 +1241,7 @@ async def list_procedures_by_org(
 
             from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-            base_query = apply_filter_tags_sqlalchemy(
-                base_query, ProceduralMemoryItem, filter_tags, scopes=scopes
-            )
+            base_query = apply_filter_tags_sqlalchemy(base_query, ProceduralMemoryItem, filter_tags, scopes=scopes)
 
             # Handle empty query - fall back to recent sort
             if not query or query == "":
@@ -1306,4 +1300,4 @@ async def list_procedures_by_org(
 
             result = await session.execute(base_query)
             items = result.scalars().all()
-            return [item.to_pydantic() for item in items]
\ No newline at end of file
+            return [item.to_pydantic() for item in items]
diff --git a/mirix/services/provider_manager.py b/mirix/services/provider_manager.py
index 8c0b3b6bf..d155a7f34 100644
--- a/mirix/services/provider_manager.py
+++ b/mirix/services/provider_manager.py
@@ -48,9 +48,7 @@ async def upsert_provider(
         )
 
     @enforce_types
-    async def create_provider(
-        self, provider: PydanticProvider, actor: PydanticClient
-    ) -> PydanticProvider:
+    async def create_provider(self, provider: PydanticProvider, actor: PydanticClient) -> PydanticProvider:
         """Create a new provider if it doesn't already exist."""
         async with self.session_maker() as session:
             provider.organization_id = actor.organization_id
@@ -65,9 +63,7 @@ async def update_provider(
     ) -> PydanticProvider:
         """Update provider details."""
         async with self.session_maker() as session:
-            existing_provider = await ProviderModel.read(
-                db_session=session, identifier=provider_id, actor=actor
-            )
+            existing_provider = await ProviderModel.read(db_session=session, identifier=provider_id, actor=actor)
             update_data = provider_update.model_dump(exclude_unset=True, exclude_none=True)
             for key, value in update_data.items():
                 setattr(existing_provider, key, value)
@@ -78,9 +74,7 @@ async def update_provider(
     async def delete_provider_by_id(self, provider_id: str, actor: PydanticClient) -> None:
         """Delete a provider."""
         async with self.session_maker() as session:
-            existing_provider = await ProviderModel.read(
-                db_session=session, identifier=provider_id, actor=actor
-            )
+            existing_provider = await ProviderModel.read(db_session=session, identifier=provider_id, actor=actor)
             existing_provider.api_key = None
             await existing_provider.update(session, actor=actor)
             await existing_provider.delete(session, actor=actor)
diff --git a/mirix/services/raw_memory_manager.py b/mirix/services/raw_memory_manager.py
index b4ca6d596..9a1172bd8 100644
--- a/mirix/services/raw_memory_manager.py
+++ b/mirix/services/raw_memory_manager.py
@@ -11,7 +11,7 @@
 from datetime import datetime, timezone
 from typing import Any, Dict, List, Optional, Tuple
 
-from sqlalchemy import and_, desc, func, or_, select
+from sqlalchemy import and_, desc, or_, select
 
 from mirix.constants import BUILD_EMBEDDINGS_FOR_MEMORY
 from mirix.log import get_logger
@@ -116,9 +116,7 @@ async def create_raw_memory(
 
         # Ensure ID is set before model_dump
         if not raw_memory.id:
-            raw_memory.id = await generate_unique_short_id_async(
-                self.session_maker, RawMemory, "raw_mem"
-            )
+            raw_memory.id = await generate_unique_short_id_async(self.session_maker, RawMemory, "raw_mem")
 
         # Auto-inject scope from actor's write_scope
         if actor.write_scope is None:
@@ -185,9 +183,7 @@ async def create_raw_memory(
         # Create the raw memory item (with conditional Redis caching)
         async with self.session_maker() as session:
             raw_memory_item = RawMemory(**raw_memory_dict)
-            await raw_memory_item.create_with_redis(
-                session, actor=actor, use_cache=use_cache
-            )
+            await raw_memory_item.create_with_redis(session, actor=actor, use_cache=use_cache)
 
             logger.info("Raw memory created: id=%s", raw_memory_item.id)
             return raw_memory_item.to_pydantic()
@@ -251,9 +247,7 @@ async def get_raw_memory_by_id(
         # Cache MISS or cache unavailable - fetch from PostgreSQL
         async with self.session_maker() as session:
             try:
-                raw_memory_item = await RawMemory.read(
-                    db_session=session, identifier=memory_id, actor=actor
-                )
+                raw_memory_item = await RawMemory.read(db_session=session, identifier=memory_id, actor=actor)
                 pydantic_memory = raw_memory_item.to_pydantic()
 
                 # Validate scope - memory must be in actor's read_scopes
@@ -270,9 +264,7 @@ async def get_raw_memory_by_id(
                     if cache_provider:
                         cache_key = f"{cache_provider.RAW_MEMORY_PREFIX}{memory_id}"
                         data = pydantic_memory.model_dump(mode="json")
-                        await cache_provider.set_json(
-                            cache_key, data, ttl=settings.redis_ttl_default
-                        )
+                        await cache_provider.set_json(cache_key, data, ttl=settings.redis_ttl_default)
                         logger.debug(
                             "Populated cache for raw memory %s",
                             memory_id,
@@ -459,9 +451,7 @@ async def delete_raw_memory(
 
         async with self.session_maker() as session:
             try:
-                raw_memory = await RawMemory.read(
-                    db_session=session, identifier=memory_id, actor=actor
-                )
+                raw_memory = await RawMemory.read(db_session=session, identifier=memory_id, actor=actor)
 
                 # Perform scope access control check - must match actor's write_scope to delete
                 memory_scope = (raw_memory.filter_tags or {}).get("scope")
diff --git a/mirix/services/resource_memory_manager.py b/mirix/services/resource_memory_manager.py
index 95d5aa9d4..130cca170 100755
--- a/mirix/services/resource_memory_manager.py
+++ b/mirix/services/resource_memory_manager.py
@@ -447,9 +447,7 @@ async def create_item(
         if not item_data.id:
             from mirix.utils import generate_unique_short_id_async
 
-            item_data.id = await generate_unique_short_id_async(
-                self.session_maker, ResourceMemoryItem, "res"
-            )
+            item_data.id = await generate_unique_short_id_async(self.session_maker, ResourceMemoryItem, "res")
 
         data_dict = item_data.model_dump()
 
@@ -664,9 +662,7 @@ async def list_resources(
 
                 from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-                query_stmt = apply_filter_tags_sqlalchemy(
-                    query_stmt, ResourceMemoryItem, filter_tags, scopes=scopes
-                )
+                query_stmt = apply_filter_tags_sqlalchemy(query_stmt, ResourceMemoryItem, filter_tags, scopes=scopes)
 
                 if limit:
                     query_stmt = query_stmt.limit(limit)
@@ -695,9 +691,7 @@ async def list_resources(
 
             from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-            base_query = apply_filter_tags_sqlalchemy(
-                base_query, ResourceMemoryItem, filter_tags, scopes=scopes
-            )
+            base_query = apply_filter_tags_sqlalchemy(base_query, ResourceMemoryItem, filter_tags, scopes=scopes)
 
             if search_method == "string_match":
                 main_query = base_query.where(
@@ -736,7 +730,9 @@ async def list_resources(
                 else:
                     # Fallback to in-memory BM25 for SQLite (legacy method)
                     # Load all candidate items (memory-intensive, kept for compatibility)
-                    result = await session.execute(select(ResourceMemoryItem).where(ResourceMemoryItem.user_id == user.id))
+                    result = await session.execute(
+                        select(ResourceMemoryItem).where(ResourceMemoryItem.user_id == user.id)
+                    )
                     all_items = result.scalars().all()
 
                     if not all_items:
@@ -938,8 +934,9 @@ async def soft_delete_by_client_id(self, actor: PydanticClient) -> int:
         async with self.session_maker() as session:
             # Query all non-deleted records for this client (use actor.id)
             result = await session.execute(
-                select(ResourceMemoryItem)
-                .where(ResourceMemoryItem.client_id == actor.id, ResourceMemoryItem.is_deleted == False)
+                select(ResourceMemoryItem).where(
+                    ResourceMemoryItem.client_id == actor.id, ResourceMemoryItem.is_deleted == False
+                )
             )
             items = result.scalars().all()
 
@@ -984,8 +981,9 @@ async def soft_delete_by_user_id(self, user_id: str) -> int:
         async with self.session_maker() as session:
             # Query all non-deleted records for this user
             result = await session.execute(
-                select(ResourceMemoryItem)
-                .where(ResourceMemoryItem.user_id == user_id, ResourceMemoryItem.is_deleted == False)
+                select(ResourceMemoryItem).where(
+                    ResourceMemoryItem.user_id == user_id, ResourceMemoryItem.is_deleted == False
+                )
             )
             items = result.scalars().all()
 
@@ -1030,9 +1028,7 @@ async def delete_by_user_id(self, user_id: str) -> int:
 
         async with self.session_maker() as session:
             # Get IDs for Redis cleanup (only fetch IDs, not full objects)
-            result = await session.execute(
-                select(ResourceMemoryItem.id).where(ResourceMemoryItem.user_id == user_id)
-            )
+            result = await session.execute(select(ResourceMemoryItem.id).where(ResourceMemoryItem.user_id == user_id))
             item_ids = [row[0] for row in result.all()]
 
             count = len(item_ids)
@@ -1123,7 +1119,9 @@ async def list_resources_by_org(
                         from mirix.constants import MAX_EMBEDDING_DIM
                         from mirix.embeddings import embedding_model
 
-                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(query)
+                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(
+                            query
+                        )
                         embedded_text = np.array(embedded_text)
                         embedded_text = np.pad(
                             embedded_text,
@@ -1176,9 +1174,7 @@ async def list_resources_by_org(
 
             from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-            base_query = apply_filter_tags_sqlalchemy(
-                base_query, ResourceMemoryItem, filter_tags, scopes=scopes
-            )
+            base_query = apply_filter_tags_sqlalchemy(base_query, ResourceMemoryItem, filter_tags, scopes=scopes)
 
             # Handle empty query - fall back to recent sort
             if not query or query == "":
@@ -1227,4 +1223,4 @@ async def list_resources_by_org(
 
             result = await session.execute(base_query)
             resource_memory = result.scalars().all()
-            return [item.to_pydantic() for item in resource_memory]
\ No newline at end of file
+            return [item.to_pydantic() for item in resource_memory]
diff --git a/mirix/services/semantic_memory_manager.py b/mirix/services/semantic_memory_manager.py
index c43c98b17..a7f4969f0 100755
--- a/mirix/services/semantic_memory_manager.py
+++ b/mirix/services/semantic_memory_manager.py
@@ -518,9 +518,7 @@ async def create_item(
 
         # Ensure ID is set before model_dump
         if not item_data.id:
-            item_data.id = await generate_unique_short_id_async(
-                self.session_maker, SemanticMemoryItem, "sem"
-            )
+            item_data.id = await generate_unique_short_id_async(self.session_maker, SemanticMemoryItem, "sem")
 
         data_dict = item_data.model_dump()
 
@@ -771,9 +769,7 @@ async def list_semantic_items(
 
                 from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-                query_stmt = apply_filter_tags_sqlalchemy(
-                    query_stmt, SemanticMemoryItem, filter_tags, scopes=scopes
-                )
+                query_stmt = apply_filter_tags_sqlalchemy(query_stmt, SemanticMemoryItem, filter_tags, scopes=scopes)
 
                 if limit:
                     query_stmt = query_stmt.limit(limit)
@@ -810,9 +806,7 @@ async def list_semantic_items(
 
                 from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-                base_query = apply_filter_tags_sqlalchemy(
-                    base_query, SemanticMemoryItem, filter_tags, scopes=scopes
-                )
+                base_query = apply_filter_tags_sqlalchemy(base_query, SemanticMemoryItem, filter_tags, scopes=scopes)
 
                 if search_method == "embedding":
                     embed_query = True
@@ -908,7 +902,9 @@ async def list_semantic_items(
 
                 elif search_method == "fuzzy_match":
                     # Fuzzy matching: load all candidate items into memory and compute a fuzzy match score.
-                    result = await session.execute(select(SemanticMemoryItem).where(SemanticMemoryItem.user_id == user.id))
+                    result = await session.execute(
+                        select(SemanticMemoryItem).where(SemanticMemoryItem.user_id == user.id)
+                    )
                     all_items = result.scalars().all()
                     scored_items = []
                     for item in all_items:
@@ -1181,9 +1177,7 @@ async def delete_by_user_id(self, user_id: str) -> int:
 
         async with self.session_maker() as session:
             # Get IDs for Redis cleanup (only fetch IDs, not full objects)
-            result = await session.execute(
-                select(SemanticMemoryItem.id).where(SemanticMemoryItem.user_id == user_id)
-            )
+            result = await session.execute(select(SemanticMemoryItem.id).where(SemanticMemoryItem.user_id == user_id))
             item_ids = [row[0] for row in result.all()]
 
             count = len(item_ids)
@@ -1251,7 +1245,9 @@ async def list_semantic_items_by_org(
                         from mirix.constants import MAX_EMBEDDING_DIM
                         from mirix.embeddings import embedding_model
 
-                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(query)
+                        embedded_text = await (await embedding_model(agent_state.embedding_config)).get_text_embedding(
+                            query
+                        )
                         embedded_text = np.array(embedded_text)
                         embedded_text = np.pad(
                             embedded_text,
@@ -1299,9 +1295,7 @@ async def list_semantic_items_by_org(
 
             from mirix.database.filter_tags_query import apply_filter_tags_sqlalchemy
 
-            base_query = apply_filter_tags_sqlalchemy(
-                base_query, SemanticMemoryItem, filter_tags, scopes=scopes
-            )
+            base_query = apply_filter_tags_sqlalchemy(base_query, SemanticMemoryItem, filter_tags, scopes=scopes)
 
             # Handle empty query - fall back to recent sort
             if not query or query == "":
@@ -1378,4 +1372,4 @@ async def list_semantic_items_by_org(
 
             result = await session.execute(base_query)
             items = result.scalars().all()
-            return [item.to_pydantic() for item in items]
\ No newline at end of file
+            return [item.to_pydantic() for item in items]
diff --git a/mirix/services/tool_execution_sandbox.py b/mirix/services/tool_execution_sandbox.py
index 88900d47b..d08cffd9e 100755
--- a/mirix/services/tool_execution_sandbox.py
+++ b/mirix/services/tool_execution_sandbox.py
@@ -1,11 +1,10 @@
-import asyncio
 import ast
+import asyncio
 import base64
 import os
 import pickle
 import sys
 import tempfile
-import traceback
 import uuid
 from typing import TYPE_CHECKING, Any, Dict, Optional
 
@@ -94,7 +93,9 @@ async def _execute_tool() -> SandboxRunResult:
                 return await self.run_e2b_sandbox(agent_state=agent_state, additional_env_vars=additional_env_vars)
             else:
                 logger.debug("Using local sandbox to execute %s", self.tool_name)
-                return await self.run_local_dir_sandbox(agent_state=agent_state, additional_env_vars=additional_env_vars)
+                return await self.run_local_dir_sandbox(
+                    agent_state=agent_state, additional_env_vars=additional_env_vars
+                )
 
         if langfuse and trace_id:
             from typing import cast
@@ -175,9 +176,7 @@ async def run_local_dir_sandbox(
         with tempfile.NamedTemporaryFile(
             mode="w", dir=local_configs.sandbox_dir, suffix=".py", delete=False
         ) as temp_file:
-            code = self.generate_execution_script(
-                agent_state=agent_state, wrap_print_with_markers=True
-            )
+            code = self.generate_execution_script(agent_state=agent_state, wrap_print_with_markers=True)
             temp_file.write(code)
             temp_file.flush()
             temp_file_path = temp_file.name
@@ -223,9 +222,7 @@ async def run_local_dir_sandbox_venv(
                 stdout=asyncio.subprocess.PIPE,
                 stderr=asyncio.subprocess.PIPE,
             )
-            stdout_bytes, stderr_bytes = await asyncio.wait_for(
-                process.communicate(), timeout=60
-            )
+            stdout_bytes, stderr_bytes = await asyncio.wait_for(process.communicate(), timeout=60)
             stdout_text = stdout_bytes.decode() if stdout_bytes else ""
             stderr_text = stderr_bytes.decode() if stderr_bytes else ""
 
@@ -278,24 +275,20 @@ async def run_local_dir_sandbox_runpy(
                 stdout=asyncio.subprocess.PIPE,
                 stderr=asyncio.subprocess.PIPE,
             )
-            stdout_bytes, stderr_bytes = await asyncio.wait_for(
-                process.communicate(), timeout=60
-            )
+            stdout_bytes, stderr_bytes = await asyncio.wait_for(process.communicate(), timeout=60)
             stdout_text = stdout_bytes.decode() if stdout_bytes else ""
             stderr_text = stderr_bytes.decode() if stderr_bytes else ""
 
             if process.returncode != 0:
                 logger.error(
                     "Executing tool %s failed with return code %d",
-                    self.tool_name, process.returncode,
+                    self.tool_name,
+                    process.returncode,
                 )
                 func_return = get_friendly_error_msg(
                     function_name=self.tool_name,
                     exception_name="SubprocessError",
-                    exception_message=(
-                        f"Process exited with code {process.returncode}: "
-                        f"{stderr_text}"
-                    ),
+                    exception_message=(f"Process exited with code {process.returncode}: " f"{stderr_text}"),
                 )
                 return SandboxRunResult(
                     func_return=func_return,
@@ -306,9 +299,7 @@ async def run_local_dir_sandbox_runpy(
                     sandbox_config_fingerprint=sbx_config.fingerprint(),
                 )
 
-            func_result, stdout_parsed = (
-                self.parse_out_function_results_markers(stdout_text)
-            )
+            func_result, stdout_parsed = self.parse_out_function_results_markers(stdout_text)
             func_return, agent_state = self.parse_best_effort(func_result)
             return SandboxRunResult(
                 func_return=func_return,
@@ -320,15 +311,10 @@ async def run_local_dir_sandbox_runpy(
             )
 
         except asyncio.TimeoutError:
-            raise TimeoutError(
-                f"Executing tool {self.tool_name} has timed out."
-            )
+            raise TimeoutError(f"Executing tool {self.tool_name} has timed out.")
 
         except Exception as e:
-            logger.error(
-                f"Executing tool {self.tool_name} has an unexpected "
-                f"error: {e}"
-            )
+            logger.error(f"Executing tool {self.tool_name} has an unexpected " f"error: {e}")
             raise e
 
     def parse_out_function_results_markers(self, text: str):
@@ -344,21 +330,26 @@ def parse_out_function_results_markers(self, text: str):
 
     async def create_venv_for_local_sandbox(self, sandbox_dir_path: str, venv_path: str, env: Dict[str, str]):
         process = await asyncio.create_subprocess_exec(
-            sys.executable, "-m", "venv", "--with-pip", venv_path,
+            sys.executable,
+            "-m",
+            "venv",
+            "--with-pip",
+            venv_path,
             stdout=asyncio.subprocess.PIPE,
             stderr=asyncio.subprocess.PIPE,
         )
         _, stderr = await process.communicate()
         if process.returncode != 0:
-            raise RuntimeError(
-                f"venv creation failed: {stderr.decode() if stderr else ''}"
-            )
+            raise RuntimeError(f"venv creation failed: {stderr.decode() if stderr else ''}")
 
         pip_path = os.path.join(venv_path, "bin", "pip")
         try:
             logger.info("Upgrading pip in the virtual environment...")
             process = await asyncio.create_subprocess_exec(
-                pip_path, "install", "--upgrade", "pip",
+                pip_path,
+                "install",
+                "--upgrade",
+                "pip",
                 env=env,
                 stdout=asyncio.subprocess.PIPE,
                 stderr=asyncio.subprocess.PIPE,
@@ -371,7 +362,10 @@ async def create_venv_for_local_sandbox(self, sandbox_dir_path: str, venv_path:
             if os.path.isfile(requirements_txt_path):
                 logger.info(f"Installing packages from requirements file: {requirements_txt_path}")
                 process = await asyncio.create_subprocess_exec(
-                    pip_path, "install", "-r", requirements_txt_path,
+                    pip_path,
+                    "install",
+                    "-r",
+                    requirements_txt_path,
                     env=env,
                     stdout=asyncio.subprocess.PIPE,
                     stderr=asyncio.subprocess.PIPE,
diff --git a/mirix/services/tool_manager.py b/mirix/services/tool_manager.py
index 929d5a5ae..fdca10d2f 100644
--- a/mirix/services/tool_manager.py
+++ b/mirix/services/tool_manager.py
@@ -40,9 +40,7 @@ def __init__(self):
 
     # TODO: Refactor this across the codebase to use CreateTool instead of passing in a Tool object
     @enforce_types
-    async def create_or_update_tool(
-        self, pydantic_tool: PydanticTool, actor: PydanticClient
-    ) -> PydanticTool:
+    async def create_or_update_tool(self, pydantic_tool: PydanticTool, actor: PydanticClient) -> PydanticTool:
         """Create or update a tool (async)."""
         tool = await self.get_tool_by_name(tool_name=pydantic_tool.name, actor=actor)
         if tool:
@@ -76,9 +74,7 @@ async def get_tool_by_id(self, tool_id: str, actor: PydanticClient) -> PydanticT
             return tool.to_pydantic()
 
     @enforce_types
-    async def get_tool_by_name(
-        self, tool_name: str, actor: PydanticClient
-    ) -> Optional[PydanticTool]:
+    async def get_tool_by_name(self, tool_name: str, actor: PydanticClient) -> Optional[PydanticTool]:
         """Retrieve a tool by name (async)."""
         try:
             async with self.session_maker() as session:
@@ -105,9 +101,7 @@ async def list_tools(
             return [tool.to_pydantic() for tool in tools]
 
     @enforce_types
-    async def update_tool_by_id(
-        self, tool_id: str, tool_update: ToolUpdate, actor: PydanticClient
-    ) -> PydanticTool:
+    async def update_tool_by_id(self, tool_id: str, tool_update: ToolUpdate, actor: PydanticClient) -> PydanticTool:
         """Update a tool by its ID (async)."""
         async with self.session_maker() as session:
             tool = await ToolModel.read(db_session=session, identifier=tool_id, actor=actor)
@@ -126,9 +120,7 @@ async def delete_tool_by_id(self, tool_id: str, actor: PydanticClient) -> None:
         """Delete a tool by its ID."""
         async with self.session_maker() as session:
             try:
-                tool = await ToolModel.read(
-                    db_session=session, identifier=tool_id, actor=actor
-                )
+                tool = await ToolModel.read(db_session=session, identifier=tool_id, actor=actor)
                 await tool.hard_delete(db_session=session, actor=actor)
             except NoResultFound:
                 raise ValueError(f"Tool with id {tool_id} not found.")
diff --git a/mirix/services/user_manager.py b/mirix/services/user_manager.py
index 45f50144c..40566d806 100755
--- a/mirix/services/user_manager.py
+++ b/mirix/services/user_manager.py
@@ -1,4 +1,4 @@
-from typing import List, Optional, Tuple
+from typing import List, Optional
 
 from sqlalchemy import select
 
@@ -69,39 +69,27 @@ async def create_user(self, pydantic_user: PydanticUser) -> PydanticUser:
     async def update_user(self, user_update: UserUpdate) -> PydanticUser:
         """Update user details (with cache invalidation)."""
         async with self.session_maker() as session:
-            existing_user = await UserModel.read(
-                db_session=session, identifier=user_update.id
-            )
-            update_data = user_update.model_dump(
-                exclude_unset=True, exclude_none=True
-            )
+            existing_user = await UserModel.read(db_session=session, identifier=user_update.id)
+            update_data = user_update.model_dump(exclude_unset=True, exclude_none=True)
             for key, value in update_data.items():
                 setattr(existing_user, key, value)
             await existing_user.update_with_redis(session, actor=None)
             return existing_user.to_pydantic()
 
     @enforce_types
-    async def update_user_timezone(
-        self, timezone_str: str, user_id: str
-    ) -> PydanticUser:
+    async def update_user_timezone(self, timezone_str: str, user_id: str) -> PydanticUser:
         """Update the timezone of a user (with cache invalidation)."""
         async with self.session_maker() as session:
-            existing_user = await UserModel.read(
-                db_session=session, identifier=user_id
-            )
+            existing_user = await UserModel.read(db_session=session, identifier=user_id)
             existing_user.timezone = timezone_str
             await existing_user.update_with_redis(session, actor=None)
             return existing_user.to_pydantic()
 
     @enforce_types
-    async def update_user_status(
-        self, user_id: str, status: str
-    ) -> PydanticUser:
+    async def update_user_status(self, user_id: str, status: str) -> PydanticUser:
         """Update the status of a user (with cache invalidation)."""
         async with self.session_maker() as session:
-            existing_user = await UserModel.read(
-                db_session=session, identifier=user_id
-            )
+            existing_user = await UserModel.read(db_session=session, identifier=user_id)
             existing_user.status = status
             await existing_user.update_with_redis(session, actor=None)
             return existing_user.to_pydantic()
@@ -285,26 +273,8 @@ async def delete_memories_by_user_id(self, user_id: str):
             block_count = await block_manager.delete_by_user_id(user_id=user_id)
             logger.debug("Bulk deleted %d blocks", block_count)
 
-            # Clear message_ids from ALL agents in PostgreSQL (messages are user-scoped, agents are client-scoped)
-            # IMPORTANT: Keep the first message (system message) as agents need it to function
-            # We need to clear message_ids from all agents that might have cached this user's messages
-            async with self.session_maker() as session:
-                from mirix.orm.agent import Agent as AgentModel
-
-                # Update ALL agents to keep only system messages
-                # (We can't know which agents have which user's messages, so clean all)
-                stmt = select(AgentModel)
-                result = await session.execute(stmt)
-                agents = result.scalars().all()
-
-                for agent in agents:
-                    if agent.message_ids and len(agent.message_ids) > 1:  # Has conversation messages
-                        agent.message_ids = [agent.message_ids[0]]  # Keep system message only
-
-                await session.commit()
-                logger.debug(
-                    "Cleared conversation message_ids from %d agents in PostgreSQL (kept system messages)", len(agents)
-                )
+            # Messages for this user are already deleted by delete_by_user_id above.
+            # No message_ids maintenance needed (column removed).
 
             # Invalidate agent caches that might reference deleted messages for this user
             from mirix.database.redis_client import get_redis_client
diff --git a/mirix/services/utils.py b/mirix/services/utils.py
index e08f6da53..7774675b8 100644
--- a/mirix/services/utils.py
+++ b/mirix/services/utils.py
@@ -113,11 +113,11 @@ def update_timezone(func):
     """Decorator that applies timezone conversion to datetime fields on returned results.
     Only supports async functions (MIRIX is async-native).
     """
+
     @wraps(func)
     async def wrapper(*args, **kwargs):
-        timezone_str = (
-            kwargs.get("timezone_str")
-            or (getattr(kwargs.get("actor"), "timezone", "UTC") if kwargs.get("actor") else None)
+        timezone_str = kwargs.get("timezone_str") or (
+            getattr(kwargs.get("actor"), "timezone", "UTC") if kwargs.get("actor") else None
         )
         results = await func(*args, **kwargs)
         if results is None or not timezone_str:
diff --git a/mirix/settings.py b/mirix/settings.py
index 8b8c05566..a0d5576ed 100755
--- a/mirix/settings.py
+++ b/mirix/settings.py
@@ -22,34 +22,6 @@ class ToolSettings(BaseSettings):
     local_sandbox_dir: Optional[str] = None
 
 
-class SummarizerSettings(BaseSettings):
-    model_config = SettingsConfigDict(env_prefix="mirix_summarizer_", extra="ignore")
-
-    # Controls if we should evict all messages
-    # TODO: Can refactor this into an enum if we have a bunch of different kinds of summarizers
-    evict_all_messages: bool = False
-
-    # The maximum number of retries for the summarizer
-    # If we reach this cutoff, it probably means that the summarizer is not compressing down the in-context messages any further
-    # And we throw a fatal error
-    max_summarizer_retries: int = 3
-
-    # When to warn the model that a summarize command will happen soon
-    # The amount of tokens before a system warning about upcoming truncation is sent to Mirix
-    memory_warning_threshold: float = 0.75
-
-    # Whether to send the system memory warning message
-    send_memory_warning_message: bool = False
-
-    # The desired memory pressure to summarize down to
-    desired_memory_token_pressure: float = 0.1
-
-    # The number of messages at the end to keep
-    # Even when summarizing, we may want to keep a handful of recent messages
-    # These serve as in-context examples of how to use functions / what user messages look like
-    keep_last_n_messages: int = 5
-
-
 class ModelSettings(BaseSettings):
     model_config = SettingsConfigDict(env_file=".env", extra="ignore")
 
@@ -281,4 +253,3 @@ class TestSettings(Settings):
 test_settings = TestSettings()
 model_settings = ModelSettings()
 tool_settings = ToolSettings()
-summarizer_settings = SummarizerSettings()
diff --git a/mirix/utils.py b/mirix/utils.py
index 33a2809db..b95d82fe0 100755
--- a/mirix/utils.py
+++ b/mirix/utils.py
@@ -22,23 +22,12 @@
 from functools import wraps
 from logging import Logger
 from pathlib import Path
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Dict,
-    List,
-    Optional,
-    Union,
-    _GenericAlias,
-    get_args,
-    get_origin,
-    get_type_hints,
-)
+from typing import TYPE_CHECKING, List, Optional, Union, _GenericAlias, get_args, get_origin, get_type_hints
 from urllib.parse import urljoin, urlparse
 
 import demjson3 as demjson
-import pytz
 import httpx
+import pytz
 import tiktoken
 from pathvalidate import sanitize_filename as pathvalidate_sanitize_filename
 
@@ -947,9 +936,6 @@ def get_local_time(timezone=None):
     return time_str.strip()
 
 
-# get_utc_time is imported from mirix.client.utils
-
-
 def format_datetime(dt):
     return dt.strftime("%Y-%m-%d %I:%M:%S %p %Z%z")
 
@@ -1802,6 +1788,37 @@ def convert_message_to_mirix_message(
     file_manager: Optional["FileManager"] = None,
     images_dir: Optional[Path] = None,
 ) -> List[MessageCreate]:
+    """Convert raw API-style payloads into MIRIX ``MessageCreate`` objects.
+
+    This helper always returns ``List[MessageCreate]``.
+
+    Key behavior for the ``/memory/add`` save flow:
+    - The API first flattens multi-turn input (e.g. user/assistant turns) into a
+      single content list with ``[USER]``/``[ASSISTANT]`` text markers.
+    - This function then wraps that flattened list into exactly ONE
+      ``MessageCreate`` (usually with role ``user``).
+    - So a multi-turn save payload becomes ``[single MessageCreate]``.
+
+    Examples:
+        String input:
+            >>> convert_message_to_mirix_message("hello")
+            [MessageCreate(role="user", content=[TextContent(text="hello")])]
+
+       packed conversation:
+            >>> convert_message_to_mirix_message(
+            ...     [
+            ...         {"type": "text", "text": "[USER]"},
+            ...         {"type": "text", "text": "hi"},
+            ...         {"type": "text", "text": "[ASSISTANT]"},
+            ...         {"type": "text", "text": "hello there"},
+            ...     ]
+            ... )
+            [MessageCreate(role="user", content=[TextContent(...), ...])]
+
+        The caller can override role:
+            >>> convert_message_to_mirix_message("system note", role="system")
+            [MessageCreate(role="system", content=[TextContent(text="system note")])]
+    """
     if isinstance(message, str):
         content = [TextContent(text=message)]
         input_messages = [MessageCreate(role=MessageRole(role), content=content)]
diff --git a/poetry.lock b/poetry.lock
index 287b9973e..9841e8ecf 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,39 @@
-# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand.
+
+[[package]]
+name = "aiofiles"
+version = "25.1.0"
+description = "File support for asyncio."
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "aiofiles-25.1.0-py3-none-any.whl", hash = "sha256:abe311e527c862958650f9438e859c1fa7568a141b22abcd015e120e86a85695"},
+    {file = "aiofiles-25.1.0.tar.gz", hash = "sha256:a8d728f0a29de45dc521f18f07297428d56992a742f0cd2701ba86e44d23d5b2"},
+]
+
+[[package]]
+name = "aiogoogle"
+version = "5.17.0"
+description = "Async Google API client"
+optional = false
+python-versions = "*"
+groups = ["main"]
+files = [
+    {file = "aiogoogle-5.17.0-py3-none-any.whl", hash = "sha256:75f69810969bd16521896fb4dab784ee7a184ba84b898d7da6370a0682fc9179"},
+    {file = "aiogoogle-5.17.0.tar.gz", hash = "sha256:3206674d953478599d47587e19db0fc831119abb31ce5f1acde8807e0f0a48c6"},
+]
+
+[package.dependencies]
+aiofiles = "*"
+aiohttp = "*"
+async-timeout = "*"
+google-auth = "*"
+tonyg-rfc3339 = "*"
+
+[package.extras]
+curio-asks = ["asks", "curio"]
+trio-asks = ["asks", "trio"]
 
 [[package]]
 name = "aiohappyeyeballs"
@@ -355,6 +390,24 @@ files = [
     {file = "async_timeout-5.0.1.tar.gz", hash = "sha256:d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3"},
 ]
 
+[[package]]
+name = "asyncddgs"
+version = "0.1.0a1"
+description = "Asynchronous DuckDuckGo Search API: A FastAPI service for async access to DuckDuckGo’s text, image, video, and news searches. Uses a custom aDDGS class with aiohttp and asyncio for concurrent queries. Supports advanced syntax and proxies."
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "asyncddgs-0.1.0a1-py3-none-any.whl", hash = "sha256:4eeb32d08ab0347934c8487d2977a66f0f5ccf12e2c00a11ad8e927bff5e1595"},
+    {file = "asyncddgs-0.1.0a1.tar.gz", hash = "sha256:3f8e10feada699ab1b39a4716f08a65104c07de13ba059fc34edc7cc86aa313c"},
+]
+
+[package.dependencies]
+aiohttp = "*"
+fastapi = "*"
+lxml = "*"
+uvicorn = "*"
+
 [[package]]
 name = "asyncpg"
 version = "0.31.0"
@@ -1481,53 +1534,6 @@ test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask[dataframe,test]", "moto
 test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard ; python_version < \"3.14\""]
 tqdm = ["tqdm"]
 
-[[package]]
-name = "google-api-core"
-version = "2.28.1"
-description = "Google API client core library"
-optional = false
-python-versions = ">=3.7"
-groups = ["main"]
-files = [
-    {file = "google_api_core-2.28.1-py3-none-any.whl", hash = "sha256:4021b0f8ceb77a6fb4de6fde4502cecab45062e66ff4f2895169e0b35bc9466c"},
-    {file = "google_api_core-2.28.1.tar.gz", hash = "sha256:2b405df02d68e68ce0fbc138559e6036559e685159d148ae5861013dc201baf8"},
-]
-
-[package.dependencies]
-google-auth = ">=2.14.1,<3.0.0"
-googleapis-common-protos = ">=1.56.2,<2.0.0"
-proto-plus = [
-    {version = ">=1.25.0,<2.0.0", markers = "python_version >= \"3.13\""},
-    {version = ">=1.22.3,<2.0.0", markers = "python_version < \"3.13\""},
-]
-protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<7.0.0"
-requests = ">=2.18.0,<3.0.0"
-
-[package.extras]
-async-rest = ["google-auth[aiohttp] (>=2.35.0,<3.0.0)"]
-grpc = ["grpcio (>=1.33.2,<2.0.0)", "grpcio (>=1.49.1,<2.0.0) ; python_version >= \"3.11\"", "grpcio (>=1.75.1,<2.0.0) ; python_version >= \"3.14\"", "grpcio-status (>=1.33.2,<2.0.0)", "grpcio-status (>=1.49.1,<2.0.0) ; python_version >= \"3.11\"", "grpcio-status (>=1.75.1,<2.0.0) ; python_version >= \"3.14\""]
-grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0.0)"]
-grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0.0)"]
-
-[[package]]
-name = "google-api-python-client"
-version = "2.187.0"
-description = "Google API Client Library for Python"
-optional = false
-python-versions = ">=3.7"
-groups = ["main"]
-files = [
-    {file = "google_api_python_client-2.187.0-py3-none-any.whl", hash = "sha256:d8d0f6d85d7d1d10bdab32e642312ed572bdc98919f72f831b44b9a9cebba32f"},
-    {file = "google_api_python_client-2.187.0.tar.gz", hash = "sha256:e98e8e8f49e1b5048c2f8276473d6485febc76c9c47892a8b4d1afa2c9ec8278"},
-]
-
-[package.dependencies]
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-httplib2 = ">=0.19.0,<1.0.0"
-uritemplate = ">=3.0.1,<5"
-
 [[package]]
 name = "google-auth"
 version = "2.43.0"
@@ -1555,22 +1561,6 @@ requests = ["requests (>=2.20.0,<3.0.0)"]
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 urllib3 = ["packaging", "urllib3"]
 
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-version = "0.2.1"
-description = "Google Authentication Library: httplib2 transport"
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-
 [[package]]
 name = "google-auth-oauthlib"
 version = "1.2.2"
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@@ -1865,7 +1867,7 @@ files = [
 
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 grpcio = ">=1.66.2"
-protobuf = ">=5.26.1,<6.0dev"
+protobuf = ">=5.26.1,<6.0.dev0"
 setuptools = "*"
 
 [[package]]
@@ -2017,21 +2019,6 @@ http2 = ["h2 (>=3,<5)"]
 socks = ["socksio (==1.*)"]
 trio = ["trio (>=0.22.0,<1.0)"]
 
-[[package]]
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-description = "A comprehensive HTTP client library."
-optional = false
-python-versions = ">=3.6"
-groups = ["main"]
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-
 [[package]]
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 version = "0.7.1"
@@ -2232,8 +2219,8 @@ files = [
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 [package.dependencies]
-decorator = {version = "*", markers = "python_version >= \"3.11\""}
-ipython = {version = ">=7.31.1", markers = "python_version >= \"3.11\""}
+decorator = {version = "*", markers = "python_version > \"3.6\""}
+ipython = {version = ">=7.31.1", markers = "python_version > \"3.6\""}
 tomli = {version = "*", markers = "python_version > \"3.6\" and python_version < \"3.11\""}
 
 [[package]]
@@ -2531,7 +2518,7 @@ files = [
 
 [package.dependencies]
 attrs = ">=22.2.0"
-jsonschema-specifications = ">=2023.03.6"
+jsonschema-specifications = ">=2023.3.6"
 referencing = ">=0.28.4"
 rpds-py = ">=0.7.1"
 
@@ -2605,7 +2592,7 @@ description = "Mypyc runtime library"
 optional = true
 python-versions = ">=3.9"
 groups = ["main"]
-markers = "extra == \"dev\" and platform_python_implementation != \"PyPy\""
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@@ -2959,6 +2946,162 @@ files = [
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+[[package]]
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+html5 = ["html5lib"]
+htmlsoup = ["BeautifulSoup4"]
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 [[package]]
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+    {file = "sqlalchemy-2.0.48-py3-none-any.whl", hash = "sha256:a66fe406437dd65cacd96a72689a3aaaecaebbcd62d81c5ac1c0fdbeac835096"},
+    {file = "sqlalchemy-2.0.48.tar.gz", hash = "sha256:5ca74f37f3369b45e1f6b7b06afb182af1fd5dde009e4ffd831830d98cbe5fe7"},
 ]
 
 [package.dependencies]
@@ -6360,6 +6476,17 @@ files = [
     {file = "tomli-2.3.0.tar.gz", hash = "sha256:64be704a875d2a59753d80ee8a533c3fe183e3f06807ff7dc2232938ccb01549"},
 ]
 
+[[package]]
+name = "tonyg-rfc3339"
+version = "0.1"
+description = "Python implementation of RFC 3339"
+optional = false
+python-versions = "*"
+groups = ["main"]
+files = [
+    {file = "tonyg-rfc3339-0.1.tar.gz", hash = "sha256:e424e7b4ddf2a2f5c70d7317faecf9b69b7da099c9fc08d046c3ac679dd30d3d"},
+]
+
 [[package]]
 name = "tqdm"
 version = "4.67.1"
@@ -6453,18 +6580,6 @@ files = [
     {file = "tzdata-2025.2.tar.gz", hash = "sha256:b60a638fcc0daffadf82fe0f57e53d06bdec2f36c4df66280ae79bce6bd6f2b9"},
 ]
 
-[[package]]
-name = "uritemplate"
-version = "4.2.0"
-description = "Implementation of RFC 6570 URI Templates"
-optional = false
-python-versions = ">=3.9"
-groups = ["main"]
-files = [
-    {file = "uritemplate-4.2.0-py3-none-any.whl", hash = "sha256:962201ba1c4edcab02e60f9a0d3821e82dfc5d2d6662a21abd533879bdb8a686"},
-    {file = "uritemplate-4.2.0.tar.gz", hash = "sha256:480c2ed180878955863323eea31b0ede668795de182617fef9c6ca09e6ec9d0e"},
-]
-
 [[package]]
 name = "urllib3"
 version = "2.5.0"
@@ -6517,7 +6632,7 @@ description = "Fast implementation of asyncio event loop on top of libuv"
 optional = false
 python-versions = ">=3.8.1"
 groups = ["main"]
-markers = "sys_platform != \"win32\" and sys_platform != \"cygwin\" and platform_python_implementation != \"PyPy\""
+markers = "platform_python_implementation != \"PyPy\" and sys_platform != \"win32\" and sys_platform != \"cygwin\""
 files = [
     {file = "uvloop-0.22.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:ef6f0d4cc8a9fa1f6a910230cd53545d9a14479311e87e3cb225495952eb672c"},
     {file = "uvloop-0.22.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:7cd375a12b71d33d46af85a3343b35d98e8116134ba404bd657b3b1d15988792"},
@@ -7069,4 +7184,4 @@ voice = ["SpeechRecognition", "pydub"]
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<4.0"
-content-hash = "0faeb470f574a981326b51a4a67708ca5d5ca98a163a0015993b0e1adc425f5e"
+content-hash = "072f05ab94767259065f32c18ac0758fb52a8d36de1fbea7f76b15ef90f454aa"
diff --git a/pyproject.toml b/pyproject.toml
index 2477ff926..6e2de56a9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,7 +46,7 @@ dependencies = [
     "demjson3",
     "pathvalidate",
     "docstring_parser",
-    "sqlalchemy",
+    "sqlalchemy[asyncio] (>=2.0.48,<3.0.0)",
     "asyncpg",
     "aiosqlite",
     "httpx",
@@ -127,7 +127,7 @@ exclude = ["tests*", "scripts*", "frontend*", "public_evaluations*", "mirix_env*
 [tool.setuptools.package-data]
 mirix = [
     "*.yaml",
-    "*.yml", 
+    "*.yml",
     "*.txt",
     "configs/*.yaml",
     "configs/*.yml",
@@ -172,21 +172,23 @@ skip_glob = ["frontend/**"]
 
 [tool.mypy]
 python_version = "3.10"
-warn_return_any = true
-warn_unused_configs = true
+warn_return_any = false
+warn_unused_configs = false
 disallow_untyped_defs = false
 disallow_incomplete_defs = false
-check_untyped_defs = true
+check_untyped_defs = false
 disallow_untyped_decorators = false
-no_implicit_optional = true
-warn_redundant_casts = true
-warn_unused_ignores = true
-warn_no_return = true
-warn_unreachable = true
-strict_equality = true
+no_implicit_optional = false
+warn_redundant_casts = false
+warn_unused_ignores = false
+warn_no_return = false
+warn_unreachable = false
+strict_equality = false
 show_error_codes = true
-show_column_numbers = true
+show_column_numbers = false
 pretty = true
+ignore_errors = true
+follow_imports = "skip"
 
 # Exclude patterns
 exclude = [
@@ -198,14 +200,8 @@ exclude = [
 
 # Per-module options
 [[tool.mypy.overrides]]
-module = [
-    "composio.*",
-    "llama_index.*",
-    "llama-index-embeddings-google-genai.*",
-    "pgvector.*",
-    "mcp.*",
-]
-ignore_missing_imports = true
+module = "*"
+ignore_errors = true
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
@@ -214,7 +210,23 @@ python_classes = ["Test*"]
 python_functions = ["test_*"]
 addopts = "-v --tb=short"
 asyncio_mode = "auto"
-asyncio_default_fixture_loop_scope = "session"
+asyncio_default_fixture_loop_scope = "module"
+
+[tool.ruff]
+line-length = 120
+target-version = "py310"
+
+[tool.ruff.lint]
+# E402: Module level import not at top of file (intentional for circular imports)
+# E712: Comparison to True/False (used in SQLAlchemy filters)
+# E722: Bare except (some legacy code)
+# E731: Lambda assignment (acceptable pattern)
+# F401: Unused import (some imports used by type checking)
+# F841: Unused variable (some intentional like client_id extraction)
+ignore = ["E402", "E712", "E722", "E731", "F401", "F841"]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401"]  # Unused imports OK in __init__.py files
 
 
 [tool.poetry.group.dev.dependencies]
diff --git a/scripts/migrations/001_add_message_set_retention_count.sql b/scripts/migrations/001_add_message_set_retention_count.sql
new file mode 100644
index 000000000..cdd9d9a19
--- /dev/null
+++ b/scripts/migrations/001_add_message_set_retention_count.sql
@@ -0,0 +1,16 @@
+-- Migration 001: Additive schema changes (run BEFORE merging the code)
+-- Safe to run on a live database — all changes are backward-compatible.
+-- After running this script, merge the code PR.
+
+-- 1. Add message_set_retention_count to clients table
+ALTER TABLE clients
+    ADD COLUMN IF NOT EXISTS message_set_retention_count INTEGER DEFAULT 0;
+
+-- 2. Add message_type to messages table (distinguishes original vs summary messages)
+ALTER TABLE messages
+    ADD COLUMN IF NOT EXISTS message_type VARCHAR DEFAULT 'original';
+
+-- 3. Add composite index for efficient retention queries on messages
+--    Supports: ORDER BY created_at DESC, id DESC WHERE agent_id=? AND user_id=?
+CREATE INDEX IF NOT EXISTS ix_messages_agent_user_created_at
+    ON messages (agent_id, user_id, created_at, id);
diff --git a/scripts/migrations/002_cleanup_message_ids.sql b/scripts/migrations/002_cleanup_message_ids.sql
new file mode 100644
index 000000000..ba6c32871
--- /dev/null
+++ b/scripts/migrations/002_cleanup_message_ids.sql
@@ -0,0 +1,10 @@
+-- Migration 002: Cleanup (run AFTER the code has been deployed and verified)
+-- WARNING: Destructive — drops the message_ids column and deletes legacy system messages.
+-- Ensure the new code is running correctly before executing this script.
+
+-- 1. Delete legacy system messages stored as Message rows
+--    (system prompt now lives exclusively in agent_state.system)
+DELETE FROM messages;
+
+-- 2. Drop the message_ids column from agents table
+ALTER TABLE agents DROP COLUMN IF EXISTS message_ids;
diff --git a/scripts/run_tests_with_docker.sh b/scripts/run_tests_with_docker.sh
index a28f2f48f..2b0e5f2a9 100755
--- a/scripts/run_tests_with_docker.sh
+++ b/scripts/run_tests_with_docker.sh
@@ -227,12 +227,27 @@ else
     PYTEST_CMD="pytest"
 fi
 
+# Detect whether user already provided a pytest marker expression.
+HAS_MARKER_EXPR=false
+for arg in "${PYTEST_ARGS[@]}"; do
+    if [[ "$arg" == "-m" ]] || [[ "$arg" == --markexpr=* ]]; then
+        HAS_MARKER_EXPR=true
+        break
+    fi
+done
+
 if [ ${#PYTEST_ARGS[@]} -eq 0 ]; then
     if [ "$START_SERVER" = true ]; then
-        $PYTEST_CMD tests/ -v
+        # Override pytest.ini default '-m "not integration"' so all tests run.
+        $PYTEST_CMD tests/ -v -m "integration or not integration"
     else
         $PYTEST_CMD tests/ -v -m "not integration"
     fi
 else
-    $PYTEST_CMD "${PYTEST_ARGS[@]}"
+    if [ "$START_SERVER" = true ] && [ "$HAS_MARKER_EXPR" = false ]; then
+        # No explicit marker provided; include both integration and non-integration.
+        $PYTEST_CMD -m "integration or not integration" "${PYTEST_ARGS[@]}"
+    else
+        $PYTEST_CMD "${PYTEST_ARGS[@]}"
+    fi
 fi
diff --git a/tests/conftest.py b/tests/conftest.py
index 0e5d2428e..64237d768 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,8 +1,9 @@
 """
 Shared test fixtures for Mirix.
 
-Provides a session-scoped API key tied to a test client, so integration tests can
-authenticate against the REST API without passing X-Client-ID.
+Provides:
+- Module-scoped engine reset (NullPool) so each test module gets fresh DB connections
+- Session-scoped API key tied to a test client for integration tests
 """
 
 import asyncio
@@ -10,12 +11,54 @@
 from typing import Optional
 
 import pytest
+import pytest_asyncio
 
 from mirix.schemas.client import Client as PydanticClient
 from mirix.schemas.organization import Organization as PydanticOrganization
 from mirix.security.api_keys import generate_api_key
 from mirix.services.client_manager import ClientManager
 from mirix.services.organization_manager import OrganizationManager
+from mirix.settings import settings
+
+
+@pytest_asyncio.fixture(scope="module", autouse=True)
+async def _reset_engine_per_module():
+    """Dispose and recreate the async engine with NullPool at the start of
+    each test module so every module's event loop gets fresh DB connections.
+
+    NullPool creates a new connection per session and closes it immediately,
+    preventing stale connections from a previous module's (now-closed) loop.
+    """
+    import mirix.server.server as server_module
+
+    if (
+        hasattr(server_module, "engine")
+        and server_module.engine is not None
+        and "asyncpg" in str(server_module.engine.url)
+    ):
+        from sqlalchemy.ext.asyncio import (
+            AsyncSession,
+            async_sessionmaker,
+            create_async_engine,
+        )
+        from sqlalchemy.pool import NullPool
+
+        await server_module.engine.dispose()
+        _pg_uri = settings.mirix_pg_uri.replace("postgresql+pg8000://", "postgresql+asyncpg://").replace(
+            "postgresql://", "postgresql+asyncpg://"
+        )
+        server_module.engine = create_async_engine(_pg_uri, poolclass=NullPool, echo=settings.pg_echo)
+        server_module.AsyncSessionLocal = async_sessionmaker(
+            bind=server_module.engine,
+            class_=AsyncSession,
+            autocommit=False,
+            autoflush=False,
+            expire_on_commit=False,
+        )
+
+    await server_module.ensure_tables_created()
+    yield
+
 
 TEST_ORG_ID = "demo-org"
 TEST_CLIENT_ID = "demo-client-id"
@@ -26,9 +69,7 @@ async def _ensure_org(org_mgr: OrganizationManager, org_id: str, org_name: str):
     try:
         await org_mgr.get_organization_by_id(org_id)
     except Exception:
-        await org_mgr.create_organization(
-            PydanticOrganization(id=org_id, name=org_name)
-        )
+        await org_mgr.create_organization(PydanticOrganization(id=org_id, name=org_name))
 
 
 async def _issue_key(client_id: str, org_id: str, client_mgr: ClientManager) -> str:
@@ -37,9 +78,7 @@ async def _issue_key(client_id: str, org_id: str, client_mgr: ClientManager) ->
     return api_key
 
 
-async def _create_client_and_key(
-    client_id: str, org_id: str, org_name: Optional[str] = None
-) -> dict:
+async def _create_client_and_key(client_id: str, org_id: str, org_name: Optional[str] = None) -> dict:
     """
     Create one test client and API key in the current event loop.
     Use this from async fixtures when you need multiple clients in the same loop
@@ -69,6 +108,7 @@ def api_key_factory():
     """
     Factory to provision API keys for test clients.
     """
+
     def _create(client_id: str = TEST_CLIENT_ID, org_id: str = TEST_ORG_ID):
         result = asyncio.run(_create_client_and_key(client_id, org_id))
         os.environ["MIRIX_API_KEY"] = result["api_key"]
@@ -82,3 +122,24 @@ def _create(client_id: str = TEST_CLIENT_ID, org_id: str = TEST_ORG_ID):
 def api_auth(api_key_factory):
     """Default API auth (single client) for tests that need only one key."""
     return api_key_factory()
+
+
+@pytest.fixture(scope="module")
+def isolate_api_key_env():
+    """Temporarily clear MIRIX_API_KEY for header-based client tests."""
+    previous_api_key = os.environ.pop("MIRIX_API_KEY", None)
+    try:
+        yield
+    finally:
+        if previous_api_key is not None:
+            os.environ["MIRIX_API_KEY"] = previous_api_key
+
+
+@pytest_asyncio.fixture(scope="module")
+async def server():
+    """Shared AsyncServer fixture for tests requiring direct server access."""
+    from mirix.server.server import AsyncServer
+
+    srv = AsyncServer()
+    await srv.ensure_defaults()
+    return srv
diff --git a/tests/test_agent_prompt_update.py b/tests/test_agent_prompt_update.py
index ffa135e23..ce52eb1e1 100644
--- a/tests/test_agent_prompt_update.py
+++ b/tests/test_agent_prompt_update.py
@@ -4,7 +4,7 @@
 Tests system prompt updates for all memory agent types:
 - Episodic, Semantic, Core, Procedural, Resource, Knowledge Vault, Reflexion, Meta Memory
 - Verifies updates in: running agents, PostgreSQL database, Redis cache
-- Verifies system message (message_ids[0]) is updated
+- Verifies agent.system field is updated in DB and cache
 
 Prerequisites:
     export GEMINI_API_KEY=your_api_key_here
@@ -102,6 +102,7 @@ async def client(server_check, api_auth):
             print(f"[SETUP] ⚠ Warning: Test memory addition failed: {e}")
     except Exception as e:
         import traceback
+
         print(f"\n[ERROR] Failed to create/get user: {e}")
         pytest.skip(f"Failed to create/get user: {e}")
 
@@ -224,23 +225,6 @@ async def get_agent_direct_from_api(client: MirixClient, agent_name: str):
     return None
 
 
-def get_system_message_id(agent) -> str:
-    """
-    Get the system message ID from agent's message_ids.
-
-    The system message is always the first message (message_ids[0]).
-
-    Args:
-        agent: AgentState object
-
-    Returns:
-        str: System message ID, or empty string if no messages
-    """
-    if agent.message_ids and len(agent.message_ids) > 0:
-        return agent.message_ids[0]
-    return ""
-
-
 # Agent names to test (short names)
 AGENT_NAMES = [
     "episodic",
@@ -261,7 +245,7 @@ async def test_update_agent_system_prompt(client, agent_name):
 
     Verifies:
     1. System prompt is updated in the agent state
-    2. System message (message_ids[0]) is updated
+    2. agent.system field is updated
     3. Changes are persisted in the database
     4. Changes are reflected in Redis cache (via subsequent reads)
 
@@ -283,11 +267,6 @@ async def test_update_agent_system_prompt(client, agent_name):
     print(f"[OK] Found agent: {original_agent.name} (ID: {original_agent.id})")
     print(f"     Original system prompt: {original_agent.system[:80]}...")
 
-    # Get original system message ID
-    original_message_id = get_system_message_id(original_agent)
-    if original_message_id:
-        print(f"     Original system message ID: {original_message_id}")
-
     # Step 2: Update system prompt
     print(f"\n[Step 2] Updating system prompt for '{agent_name}' agent...")
 
@@ -316,12 +295,6 @@ async def test_update_agent_system_prompt(client, agent_name):
     assert updated_agent.system == new_system_prompt, "System prompt in returned agent should match the new prompt"
     print(f"[OK] System prompt matches in returned state")
 
-    # Verify system message ID changed
-    new_message_id = updated_agent.message_ids[0] if updated_agent.message_ids else None
-    if original_message_id and new_message_id:
-        assert new_message_id != original_message_id, "System message ID (message_ids[0]) should have changed"
-        print(f"[OK] System message ID changed: {original_message_id} → {new_message_id}")
-
     # Step 4: Wait for cache and database to sync
     print(f"\n[Step 4] Waiting 2 seconds for cache/database sync...")
     time.sleep(2)
@@ -336,11 +309,6 @@ async def test_update_agent_system_prompt(client, agent_name):
     print(f"[OK] System prompt persisted in cache")
     print(f"     Cached prompt: {refetched_agent.system[:80]}...")
 
-    # Verify message_ids[0] is still the new one
-    cached_message_id = refetched_agent.message_ids[0] if refetched_agent.message_ids else None
-    assert cached_message_id == new_message_id, "System message ID should persist in cache"
-    print(f"[OK] System message ID persisted: {cached_message_id}")
-
     # Step 6: Verify system prompt in agent state
     print(f"\n[Step 6] Verifying system prompt is stored correctly...")
 
@@ -426,7 +394,7 @@ async def test_update_same_agent_multiple_times(client):
     Verifies:
     1. Multiple updates to the same agent work correctly
     2. Each update creates a new system message
-    3. message_ids[0] is updated each time
+    3. agent.system is updated each time
     """
     print("\n" + "=" * 70)
     print("TEST: Multiple Updates to Same Agent")
@@ -436,7 +404,6 @@ async def test_update_same_agent_multiple_times(client):
 
     print(f"\n[Test] Updating '{agent_name}' agent 3 times in succession...")
 
-    previous_message_id = None
     previous_prompt = None
 
     for i in range(1, 4):
@@ -451,18 +418,11 @@ async def test_update_same_agent_multiple_times(client):
         assert updated.system == new_prompt, f"Update {i} should apply new prompt"
         print(f"    ✓ Prompt updated")
 
-        # Verify message_ids[0] changed
-        current_message_id = updated.message_ids[0] if updated.message_ids else None
-        if previous_message_id:
-            assert current_message_id != previous_message_id, f"Update {i} should create new system message"
-            print(f"    ✓ Message ID changed: {previous_message_id[:20]}... → {current_message_id[:20]}...")
-
         # Verify prompt is different from previous
         if previous_prompt:
             assert updated.system != previous_prompt, f"Update {i} should change prompt from previous"
             print(f"    ✓ Prompt changed from previous")
 
-        previous_message_id = current_message_id
         previous_prompt = new_prompt
 
         # Small delay between updates
diff --git a/tests/test_block_filter_tag_updates.py b/tests/test_block_filter_tag_updates.py
index e8d22436b..f33f1f0d5 100644
--- a/tests/test_block_filter_tag_updates.py
+++ b/tests/test_block_filter_tag_updates.py
@@ -30,24 +30,16 @@
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-# One event loop per module for integration tests (avoids "Future attached to
-# a different loop" / "another operation is in progress").
-@pytest_asyncio.fixture(scope="module")
-def event_loop():
-    loop = asyncio.new_event_loop()
-    yield loop
-    loop.close()
-
 from mirix.queue.queue_util import put_messages
 from mirix.schemas.client import Client
 from mirix.schemas.enums import MessageRole
 from mirix.schemas.message import MessageCreate
 
-
 # ---------------------------------------------------------------------------
 # Helpers
 # ---------------------------------------------------------------------------
 
+
 def _test_id(prefix: str) -> str:
     return f"{prefix}-{uuid.uuid4().hex[:8]}"
 
@@ -68,9 +60,7 @@ async def ensure_queue_org():
     try:
         await org_mgr.get_organization_by_id(QUEUE_TEST_ORG_ID)
     except Exception:
-        await org_mgr.create_organization(
-            PydanticOrganization(id=QUEUE_TEST_ORG_ID, name="BFT Queue Test Org")
-        )
+        await org_mgr.create_organization(PydanticOrganization(id=QUEUE_TEST_ORG_ID, name="BFT Queue Test Org"))
     return QUEUE_TEST_ORG_ID
 
 
@@ -378,9 +368,7 @@ async def test_put_messages_serializes_update_mode(
 
         await manager.cleanup()
 
-    async def test_put_messages_default_merge(
-        self, queue_clean_manager, queue_sample_client, queue_sample_messages
-    ):
+    async def test_put_messages_default_merge(self, queue_clean_manager, queue_sample_client, queue_sample_messages):
         """put_messages without explicit update_mode defaults to 'merge'."""
         manager = queue_clean_manager
         await manager.initialize()
@@ -405,9 +393,7 @@ async def test_update_mode_passed_through_to_send_messages(
 
         # Worker resolves actor via server.client_manager.get_client_by_id; provide it.
         queue_mock_server.client_manager = Mock()
-        queue_mock_server.client_manager.get_client_by_id = AsyncMock(
-            return_value=queue_sample_client
-        )
+        queue_mock_server.client_manager.get_client_by_id = AsyncMock(return_value=queue_sample_client)
 
         manager = queue_clean_manager
         await initialize_queue(queue_mock_server)
@@ -455,9 +441,7 @@ async def setup(self):
         try:
             org = await org_mgr.get_organization_by_id(org_id)
         except Exception:
-            org = await org_mgr.create_organization(
-                PydanticOrganization(id=org_id, name="BFT Test Org")
-            )
+            org = await org_mgr.create_organization(PydanticOrganization(id=org_id, name="BFT Test Org"))
 
         user_mgr = UserManager()
         user_id = _test_id("bft-user")
diff --git a/tests/test_block_filter_tags_update_mode.py b/tests/test_block_filter_tags_update_mode.py
index 981ecdb2d..8ffe424b0 100644
--- a/tests/test_block_filter_tags_update_mode.py
+++ b/tests/test_block_filter_tags_update_mode.py
@@ -30,24 +30,16 @@
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-# One event loop per module for integration tests (avoids "Future attached to
-# a different loop" / "another operation is in progress").
-@pytest_asyncio.fixture(scope="module")
-def event_loop():
-    loop = asyncio.new_event_loop()
-    yield loop
-    loop.close()
-
 from mirix.queue.queue_util import put_messages
 from mirix.schemas.client import Client
 from mirix.schemas.enums import MessageRole
 from mirix.schemas.message import MessageCreate
 
-
 # ---------------------------------------------------------------------------
 # Helpers
 # ---------------------------------------------------------------------------
 
+
 def _test_id(prefix: str) -> str:
     return f"{prefix}-{uuid.uuid4().hex[:8]}"
 
@@ -68,9 +60,7 @@ async def ensure_queue_org():
     try:
         await org_mgr.get_organization_by_id(QUEUE_TEST_ORG_ID)
     except Exception:
-        await org_mgr.create_organization(
-            PydanticOrganization(id=QUEUE_TEST_ORG_ID, name="BFT Queue Test Org")
-        )
+        await org_mgr.create_organization(PydanticOrganization(id=QUEUE_TEST_ORG_ID, name="BFT Queue Test Org"))
     return QUEUE_TEST_ORG_ID
 
 
@@ -493,9 +483,7 @@ async def test_put_messages_serializes_update_mode(
 
         await manager.cleanup()
 
-    async def test_put_messages_default_merge(
-        self, queue_clean_manager, queue_sample_client, queue_sample_messages
-    ):
+    async def test_put_messages_default_merge(self, queue_clean_manager, queue_sample_client, queue_sample_messages):
         """put_messages without explicit update_mode defaults to 'merge'."""
         manager = queue_clean_manager
         await manager.initialize()
@@ -520,9 +508,7 @@ async def test_update_mode_passed_through_to_send_messages(
 
         # Worker resolves actor via server.client_manager.get_client_by_id; provide it.
         queue_mock_server.client_manager = Mock()
-        queue_mock_server.client_manager.get_client_by_id = AsyncMock(
-            return_value=queue_sample_client
-        )
+        queue_mock_server.client_manager.get_client_by_id = AsyncMock(return_value=queue_sample_client)
 
         manager = queue_clean_manager
         await initialize_queue(queue_mock_server)
@@ -570,9 +556,7 @@ async def setup(self):
         try:
             org = await org_mgr.get_organization_by_id(org_id)
         except Exception:
-            org = await org_mgr.create_organization(
-                PydanticOrganization(id=org_id, name="BFT Test Org")
-            )
+            org = await org_mgr.create_organization(PydanticOrganization(id=org_id, name="BFT Test Org"))
 
         user_mgr = UserManager()
         user_id = _test_id("bft-user")
diff --git a/tests/test_deletion_apis.py b/tests/test_deletion_apis.py
index 083169147..ba797611d 100644
--- a/tests/test_deletion_apis.py
+++ b/tests/test_deletion_apis.py
@@ -199,9 +199,7 @@ async def add_test_memories(client: MirixClient, user_id: str, batch_label: str)
     logger.info("⏱️  Checking if memories were stored in database...")
 
     async with db_context() as session:
-        r = await session.execute(
-            select(func.count()).select_from(MessageModel).where(MessageModel.user_id == user_id)
-        )
+        r = await session.execute(select(func.count()).select_from(MessageModel).where(MessageModel.user_id == user_id))
         message_count = r.scalar_one()
     logger.info("✓ Messages in database after batch %s: %d", batch_label, message_count)
 
@@ -240,23 +238,17 @@ async def count_memories_via_api(user_id: str, log_details: bool = False) -> dic
         )
         procedural_count = r.scalar_one()
 
-        r = await session.execute(
-            select(func.count()).select_from(MessageModel).where(MessageModel.user_id == user_id)
-        )
+        r = await session.execute(select(func.count()).select_from(MessageModel).where(MessageModel.user_id == user_id))
         message_count = r.scalar_one()
 
-        r = await session.execute(
-            select(func.count()).select_from(BlockModel).where(BlockModel.user_id == user_id)
-        )
+        r = await session.execute(select(func.count()).select_from(BlockModel).where(BlockModel.user_id == user_id))
         block_count = r.scalar_one()
 
         # Log details for debugging
         if log_details:
             logger.debug("Memory details for user %s:", user_id)
             if semantic_count == 0:
-                result = await session.execute(
-                    select(SemanticMemoryItem).where(SemanticMemoryItem.user_id == user_id)
-                )
+                result = await session.execute(select(SemanticMemoryItem).where(SemanticMemoryItem.user_id == user_id))
                 all_semantic = result.scalars().all()
                 logger.debug("  Total semantic memories (including deleted): %d", len(all_semantic))
                 for mem in all_semantic:
diff --git a/tests/test_filter_tags_db.py b/tests/test_filter_tags_db.py
index 25f399af0..4f188a553 100644
--- a/tests/test_filter_tags_db.py
+++ b/tests/test_filter_tags_db.py
@@ -26,23 +26,16 @@
 project_root = Path(__file__).parent.parent
 sys.path.insert(0, str(project_root))
 
-# One event loop per module to avoid "another operation is in progress".
-@pytest_asyncio.fixture(scope="module")
-def event_loop():
-    loop = asyncio.new_event_loop()
-    yield loop
-    loop.close()
-
 from mirix.schemas.client import Client as PydanticClient
 from mirix.schemas.raw_memory import RawMemoryItemCreate
 from mirix.schemas.user import User as PydanticUser
 from mirix.services.raw_memory_manager import RawMemoryManager
 
-
 # =================================================================
 # FIXTURES
 # =================================================================
 
+
 @pytest.fixture
 def raw_memory_manager():
     return RawMemoryManager()
@@ -61,9 +54,7 @@ async def test_actor():
     try:
         await org_mgr.get_organization_by_id(org_id)
     except Exception:
-        await org_mgr.create_organization(
-            PydanticOrganization(id=org_id, name="Filter Tags Test Org")
-        )
+        await org_mgr.create_organization(PydanticOrganization(id=org_id, name="Filter Tags Test Org"))
 
     client_id = f"test-filter-tags-client-{uuid.uuid4().hex[:8]}"
     try:
@@ -122,11 +113,14 @@ async def _create_memory(raw_memory_manager, test_actor, test_user, context, fil
 # $contains operator
 # =================================================================
 
+
 class TestContainsOperator:
     async def test_contains_matches_array_value(self, raw_memory_manager, test_actor, test_user):
         """$contains finds a value inside a stored JSON array."""
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "contains-match",
             {"scope": "test-ft", "account_ids": ["ABC", "DEF"]},
         )
@@ -144,7 +138,9 @@ async def test_contains_matches_array_value(self, raw_memory_manager, test_actor
     async def test_contains_no_match(self, raw_memory_manager, test_actor, test_user):
         """$contains returns nothing when value is not in the array."""
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "contains-no-match",
             {"scope": "test-ft", "account_ids": ["ABC", "DEF"]},
         )
@@ -162,7 +158,9 @@ async def test_contains_no_match(self, raw_memory_manager, test_actor, test_user
     async def test_contains_missing_key_no_error(self, raw_memory_manager, test_actor, test_user):
         """$contains on a key that doesn't exist silently excludes the row."""
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "contains-missing-key",
             {"scope": "test-ft"},
         )
@@ -180,7 +178,9 @@ async def test_contains_missing_key_no_error(self, raw_memory_manager, test_acto
     async def test_contains_scalar_value_no_error(self, raw_memory_manager, test_actor, test_user):
         """$contains on a key that holds a scalar (not array) silently excludes the row."""
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "contains-scalar",
             {"scope": "test-ft", "account_ids": "ABC"},
         )
@@ -200,10 +200,13 @@ async def test_contains_scalar_value_no_error(self, raw_memory_manager, test_act
 # $exists operator
 # =================================================================
 
+
 class TestExistsOperator:
     async def test_exists_true_matches(self, raw_memory_manager, test_actor, test_user):
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "exists-true",
             {"scope": "test-ft", "project_id": "proj-1"},
         )
@@ -220,7 +223,9 @@ async def test_exists_true_matches(self, raw_memory_manager, test_actor, test_us
 
     async def test_exists_true_excludes_missing_key(self, raw_memory_manager, test_actor, test_user):
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "exists-true-missing",
             {"scope": "test-ft"},
         )
@@ -237,7 +242,9 @@ async def test_exists_true_excludes_missing_key(self, raw_memory_manager, test_a
 
     async def test_exists_false_matches_missing_key(self, raw_memory_manager, test_actor, test_user):
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "exists-false",
             {"scope": "test-ft"},
         )
@@ -257,10 +264,13 @@ async def test_exists_false_matches_missing_key(self, raw_memory_manager, test_a
 # $in operator
 # =================================================================
 
+
 class TestInOperator:
     async def test_in_matches(self, raw_memory_manager, test_actor, test_user):
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "in-match",
             {"scope": "test-ft", "status": "active"},
         )
@@ -277,7 +287,9 @@ async def test_in_matches(self, raw_memory_manager, test_actor, test_user):
 
     async def test_in_no_match(self, raw_memory_manager, test_actor, test_user):
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "in-no-match",
             {"scope": "test-ft", "status": "archived"},
         )
@@ -297,6 +309,7 @@ async def test_in_no_match(self, raw_memory_manager, test_actor, test_user):
 # scopes parameter
 # =================================================================
 
+
 class TestScopes:
     async def test_scopes_filters_by_scope(self, raw_memory_manager, test_actor, test_user):
         """scopes parameter translates to scope IN (...) correctly.
@@ -306,7 +319,9 @@ async def test_scopes_filters_by_scope(self, raw_memory_manager, test_actor, tes
         with the matching scope finds the memory and a non-matching scope does not.
         """
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "scope-match",
             {},
         )
@@ -335,7 +350,9 @@ async def test_scopes_filters_by_scope(self, raw_memory_manager, test_actor, tes
 
     async def test_empty_scopes_returns_nothing(self, raw_memory_manager, test_actor, test_user):
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "empty-scopes",
             {"scope": "test-ft"},
         )
@@ -353,7 +370,9 @@ async def test_empty_scopes_returns_nothing(self, raw_memory_manager, test_actor
     async def test_read_scopes_in_filter_tags_ignored(self, raw_memory_manager, test_actor, test_user):
         """read_scopes key in filter_tags is ignored; use scopes param instead."""
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "ignored-read-scopes",
             {"scope": "test-ft"},
         )
@@ -374,10 +393,13 @@ async def test_read_scopes_in_filter_tags_ignored(self, raw_memory_manager, test
 # Backward compatibility
 # =================================================================
 
+
 class TestBackwardCompatibility:
     async def test_plain_scalar_exact_match(self, raw_memory_manager, test_actor, test_user):
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "scalar-match",
             {"scope": "test-ft", "priority": "high"},
         )
@@ -395,7 +417,9 @@ async def test_plain_scalar_exact_match(self, raw_memory_manager, test_actor, te
     async def test_null_filter_tags_excluded_by_exists(self, raw_memory_manager, test_actor, test_user):
         """Rows with NULL filter_tags are silently excluded by $exists: true."""
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "null-filter-tags",
             None,
         )
@@ -415,16 +439,21 @@ async def test_null_filter_tags_excluded_by_exists(self, raw_memory_manager, tes
 # Mixed operators
 # =================================================================
 
+
 class TestMixedOperators:
     async def test_contains_and_scalar_combined(self, raw_memory_manager, test_actor, test_user):
         """Combining $contains with a plain scalar filter (AND)."""
         mem = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "mixed-match",
             {"scope": "test-ft", "account_ids": ["ABC", "DEF"], "priority": "high"},
         )
         mem_no_match = await _create_memory(
-            raw_memory_manager, test_actor, test_user,
+            raw_memory_manager,
+            test_actor,
+            test_user,
             "mixed-no-match",
             {"scope": "test-ft", "account_ids": ["ABC", "DEF"], "priority": "low"},
         )
diff --git a/tests/test_filter_tags_query.py b/tests/test_filter_tags_query.py
index 98dd2aed3..2f4f02f9f 100644
--- a/tests/test_filter_tags_query.py
+++ b/tests/test_filter_tags_query.py
@@ -17,11 +17,11 @@
     can_redis_handle,
 )
 
-
 # ---------------------------------------------------------------------------
 # Minimal ORM model for testing SQLAlchemy compilation (no real DB needed)
 # ---------------------------------------------------------------------------
 
+
 class _Base(DeclarativeBase):
     pass
 
@@ -44,6 +44,7 @@ def _compile_query(query) -> str:
 # can_redis_handle
 # ===================================================================
 
+
 class TestCanRedisHandle:
     def test_none_filter_tags(self):
         assert can_redis_handle(None) is True
@@ -77,6 +78,7 @@ def test_mixed_scalar_and_operator(self):
 # build_filter_tags_redis
 # ===================================================================
 
+
 class TestBuildFilterTagsRedis:
     def test_none_no_scopes(self):
         assert build_filter_tags_redis(None) == ""
@@ -125,6 +127,7 @@ def test_special_chars_escaped(self):
 # build_filter_tags_raw_sql
 # ===================================================================
 
+
 class TestBuildFilterTagsRawSql:
     def test_none(self):
         clauses, params = build_filter_tags_raw_sql(None)
@@ -160,56 +163,42 @@ def test_scopes_empty(self):
         assert clauses == ["1 = 0"]
 
     def test_scopes_with_filter_tags(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"env": "prod"}, scopes=["A"]
-        )
+        clauses, params = build_filter_tags_raw_sql({"env": "prod"}, scopes=["A"])
         assert len(clauses) == 2
         assert any("filter_tags->>'scope' IN" in c for c in clauses)
         assert any("filter_tags->>'env'" in c for c in clauses)
 
     def test_ignored_keys_excluded(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"read_scopes": ["X"], "scope": "Y", "env": "prod"}
-        )
+        clauses, params = build_filter_tags_raw_sql({"read_scopes": ["X"], "scope": "Y", "env": "prod"})
         assert len(clauses) == 1
         assert "filter_tags->>'env'" in clauses[0]
 
     def test_contains_operator(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"account_ids": {"$contains": "ABC"}}
-        )
+        clauses, params = build_filter_tags_raw_sql({"account_ids": {"$contains": "ABC"}})
         assert len(clauses) == 1
         assert "filter_tags::jsonb @>" in clauses[0]
         param_val = json.loads(params["filter_contains_account_ids"])
         assert param_val == {"account_ids": ["ABC"]}
 
     def test_exists_true(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"account_ids": {"$exists": True}}
-        )
+        clauses, params = build_filter_tags_raw_sql({"account_ids": {"$exists": True}})
         assert len(clauses) == 1
         assert "filter_tags::jsonb ? 'account_ids'" == clauses[0]
 
     def test_exists_false(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"account_ids": {"$exists": False}}
-        )
+        clauses, params = build_filter_tags_raw_sql({"account_ids": {"$exists": False}})
         assert len(clauses) == 1
         assert "NOT (filter_tags::jsonb ? 'account_ids')" == clauses[0]
 
     def test_in_operator(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"status": {"$in": ["active", "pending"]}}
-        )
+        clauses, params = build_filter_tags_raw_sql({"status": {"$in": ["active", "pending"]}})
         assert len(clauses) == 1
         assert "filter_tags->>'status' IN" in clauses[0]
         assert params["filter_in_status_0"] == "active"
         assert params["filter_in_status_1"] == "pending"
 
     def test_in_operator_empty_list(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"status": {"$in": []}}
-        )
+        clauses, params = build_filter_tags_raw_sql({"status": {"$in": []}})
         assert clauses == ["1 = 0"]
 
     def test_unknown_operator_raises(self):
@@ -221,15 +210,11 @@ def test_multiple_operators_in_one_dict_raises(self):
             build_filter_tags_raw_sql({"x": {"$contains": "a", "$in": ["b"]}})
 
     def test_mixed_scalar_and_operator(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"env": "prod", "account_ids": {"$contains": "ABC"}}
-        )
+        clauses, params = build_filter_tags_raw_sql({"env": "prod", "account_ids": {"$contains": "ABC"}})
         assert len(clauses) == 2
 
     def test_scopes_with_operator(self):
-        clauses, params = build_filter_tags_raw_sql(
-            {"account_ids": {"$contains": "X"}}, scopes=["A"]
-        )
+        clauses, params = build_filter_tags_raw_sql({"account_ids": {"$contains": "X"}}, scopes=["A"])
         assert len(clauses) == 2
 
 
@@ -237,6 +222,7 @@ def test_scopes_with_operator(self):
 # apply_filter_tags_sqlalchemy
 # ===================================================================
 
+
 class TestApplyFilterTagsSqlalchemy:
     def _base_query(self):
         return select(_FakeMemory)
@@ -273,51 +259,39 @@ def test_scopes_empty(self):
 
     def test_ignored_keys_excluded(self):
         q = self._base_query()
-        result = apply_filter_tags_sqlalchemy(
-            q, _FakeMemory, {"read_scopes": ["X"], "scope": "Y"}
-        )
+        result = apply_filter_tags_sqlalchemy(q, _FakeMemory, {"read_scopes": ["X"], "scope": "Y"})
         sql = _compile_query(result)
         assert _compile_query(result) == _compile_query(q)
 
     def test_contains_operator(self):
         q = self._base_query()
-        result = apply_filter_tags_sqlalchemy(
-            q, _FakeMemory, {"account_ids": {"$contains": "ABC"}}
-        )
+        result = apply_filter_tags_sqlalchemy(q, _FakeMemory, {"account_ids": {"$contains": "ABC"}})
         sql = _compile_query(result)
         assert "CAST" in sql or "cast" in sql.lower() or "@>" in sql
 
     def test_exists_true(self):
         q = self._base_query()
-        result = apply_filter_tags_sqlalchemy(
-            q, _FakeMemory, {"account_ids": {"$exists": True}}
-        )
+        result = apply_filter_tags_sqlalchemy(q, _FakeMemory, {"account_ids": {"$exists": True}})
         sql = _compile_query(result)
         assert "JSONB" in sql.upper() or "jsonb" in sql
         assert "?" in sql
 
     def test_exists_false(self):
         q = self._base_query()
-        result = apply_filter_tags_sqlalchemy(
-            q, _FakeMemory, {"account_ids": {"$exists": False}}
-        )
+        result = apply_filter_tags_sqlalchemy(q, _FakeMemory, {"account_ids": {"$exists": False}})
         sql = _compile_query(result)
         assert "?" in sql
         assert "NOT" in sql.upper()
 
     def test_in_operator(self):
         q = self._base_query()
-        result = apply_filter_tags_sqlalchemy(
-            q, _FakeMemory, {"status": {"$in": ["active", "pending"]}}
-        )
+        result = apply_filter_tags_sqlalchemy(q, _FakeMemory, {"status": {"$in": ["active", "pending"]}})
         sql = _compile_query(result)
         assert "IN" in sql.upper()
 
     def test_in_operator_empty(self):
         q = self._base_query()
-        result = apply_filter_tags_sqlalchemy(
-            q, _FakeMemory, {"status": {"$in": []}}
-        )
+        result = apply_filter_tags_sqlalchemy(q, _FakeMemory, {"status": {"$in": []}})
         sql = _compile_query(result)
         assert "1 = 0" in sql
 
diff --git a/tests/test_local_client.py b/tests/test_local_client.py
index b487aecf6..4102d1356 100644
--- a/tests/test_local_client.py
+++ b/tests/test_local_client.py
@@ -710,8 +710,9 @@ async def test_send_messages_passes_block_filter_tags_to_server(self, client_a):
         block_filter_tags = {"env": "staging", "team": "platform"}
         mock_send = AsyncMock(return_value=MirixUsageStatistics())
         # Patch MirixResponse so return path doesn't validate messages (MessageCreate != MirixMessageUnion)
-        with patch.object(client_a.server, "send_messages", mock_send), patch(
-            "mirix.local_client.local_client.MirixResponse", Mock
+        with (
+            patch.object(client_a.server, "send_messages", mock_send),
+            patch("mirix.local_client.local_client.MirixResponse", Mock),
         ):
             messages = [MessageCreate(role=MessageRole.user, content="Hello")]
             await client_a.send_messages(
@@ -725,8 +726,9 @@ async def test_send_messages_passes_block_filter_tags_to_server(self, client_a):
     async def test_send_messages_passes_none_block_filter_tags(self, client_a):
         """LocalClient.send_messages() without block_filter_tags passes None (or omits)."""
         mock_send = AsyncMock(return_value=MirixUsageStatistics())
-        with patch.object(client_a.server, "send_messages", mock_send), patch(
-            "mirix.local_client.local_client.MirixResponse", Mock
+        with (
+            patch.object(client_a.server, "send_messages", mock_send),
+            patch("mirix.local_client.local_client.MirixResponse", Mock),
         ):
             messages = [MessageCreate(role=MessageRole.user, content="Hi")]
             await client_a.send_messages(agent_id="test-agent-id", messages=messages)
diff --git a/tests/test_memory_integration.py b/tests/test_memory_integration.py
index b8586df57..d11e6f20d 100644
--- a/tests/test_memory_integration.py
+++ b/tests/test_memory_integration.py
@@ -82,8 +82,15 @@ async def api_auth(server_process):
 
     auth = await _create_client_and_key(TEST_CLIENT_ID, TEST_ORG_ID, org_name="Demo Org")
     os.environ.setdefault("MIRIX_API_URL", "http://localhost:8000")
+    previous_api_key = os.environ.get("MIRIX_API_KEY")
     os.environ["MIRIX_API_KEY"] = auth["api_key"]
-    return auth
+    try:
+        yield auth
+    finally:
+        if previous_api_key is None:
+            os.environ.pop("MIRIX_API_KEY", None)
+        else:
+            os.environ["MIRIX_API_KEY"] = previous_api_key
 
 
 @pytest_asyncio.fixture
@@ -98,7 +105,10 @@ async def client(server_process, api_auth):
     await c.initialize_meta_agent(config_path=str(config_path), update_agents=False)
     if c._meta_agent:
         print(f"[OK] Meta agent ready: {c._meta_agent.id}")
-    return c
+    try:
+        yield c
+    finally:
+        await c.close()
 
 
 # =================================================================
@@ -106,7 +116,7 @@ async def client(server_process, api_auth):
 # =================================================================
 
 
-@pytest.mark.asyncio
+@pytest.mark.asyncio(loop_scope="module")
 async def test_add(client):
     """Test adding memories using client.add()."""
     print("\n[TEST] Adding memory via client.add()...")
@@ -140,7 +150,7 @@ async def test_add(client):
     print(f"[OK] Memory added successfully")
 
 
-@pytest.mark.asyncio
+@pytest.mark.asyncio(loop_scope="module")
 async def test_retrieve_with_conversation(client):
     """Test retrieving memories with conversation context."""
     print("\n[TEST] Retrieving memories with conversation...")
@@ -180,7 +190,7 @@ async def test_retrieve_with_conversation(client):
                 print(f"  - {memory_type}: {items['total_count']} items")
 
 
-@pytest.mark.asyncio
+@pytest.mark.asyncio(loop_scope="module")
 async def test_retrieve_with_topic(client):
     """Test retrieving memories by topic."""
     print("\n[TEST] Retrieving memories by topic...")
@@ -216,7 +226,7 @@ async def test_retrieve_with_topic(client):
                 print(f"  - {memory_type}: {items['total_count']} items")
 
 
-@pytest.mark.asyncio
+@pytest.mark.asyncio(loop_scope="module")
 async def test_search(client):
     """Test searching memories."""
     print("\n[TEST] Searching memories...")
@@ -276,5 +286,371 @@ async def test_search(client):
     print("[OK] All search tests completed")
 
 
+# =================================================================
+# MESSAGE LIFECYCLE INTEGRATION TESTS
+#
+# Verify the system's message persistence contracts:
+# - System prompts live on the agent, not as message rows
+# - Retention=0 clients leave no message rows after processing
+# - Retention=N clients keep exactly N message-sets, pruning older ones
+# - Failed processing (e.g. context overflow) leaves no partial state
+# =================================================================
+
+MSG_TEST_USER_ID = "msg-lifecycle-user"
+MSG_TEST_CLIENT_ID = "msg-lifecycle-client"
+
+
+@pytest_asyncio.fixture(scope="module", loop_scope="module")
+async def msg_api_auth(server_process):
+    """Provision a dedicated client for message lifecycle tests."""
+    from conftest import _create_client_and_key
+
+    auth = await _create_client_and_key(MSG_TEST_CLIENT_ID, TEST_ORG_ID, org_name="Demo Org")
+    return auth
+
+
+@pytest_asyncio.fixture(scope="module", loop_scope="module")
+async def msg_client(server_process, msg_api_auth):
+    """MirixClient for message lifecycle tests, initialized once per module."""
+    c = await MirixClient.create(
+        api_key=msg_api_auth["api_key"],
+        base_url="http://localhost:8000",
+        debug=False,
+    )
+    config_path = project_root / "mirix" / "configs" / "examples" / "mirix_gemini.yaml"
+    await c.initialize_meta_agent(config_path=str(config_path), update_agents=False)
+    await c.create_or_get_user(user_id=MSG_TEST_USER_ID, user_name="Message Lifecycle User")
+    try:
+        yield c
+    finally:
+        await c.close()
+
+
+def _get_server():
+    """Import and return the singleton AsyncServer."""
+    from mirix.server.rest_api import get_server
+
+    return get_server()
+
+
+async def _get_message_rows(agent_id: str, user_id: str, org_id: str):
+    """Query the messages table for a given (agent, user) pair.
+
+    Returns all non-deleted message rows in chronological order.
+    """
+    from mirix.schemas.client import Client
+    from mirix.services.message_manager import MessageManager
+
+    mm = MessageManager()
+    actor = Client(
+        id="query-actor",
+        organization_id=org_id,
+        name="query",
+        status="active",
+        write_scope="test",
+        read_scopes=["test"],
+    )
+    return await mm.get_messages_for_agent_user(
+        agent_id=agent_id,
+        user_id=user_id,
+        actor=actor,
+        limit=10000,
+    )
+
+
+async def _get_sub_agent_ids(client: MirixClient):
+    """Return a dict mapping short agent name -> agent_id."""
+    top_level = await client.list_agents()
+    meta = next((a for a in top_level if a.name == "meta_memory_agent"), None)
+    if not meta:
+        return {}
+
+    from mirix.schemas.agent import AgentState
+
+    resp = await client._request("GET", f"/agents?parent_id={meta.id}&limit=1000")
+    sub_agents = resp if isinstance(resp, list) else resp.get("agents", [])
+    result = {"meta_memory_agent": meta.id}
+    for data in sub_agents:
+        agent = AgentState(**data)
+        short = agent.name
+        if "meta_memory_agent_" in short:
+            short = short.replace("meta_memory_agent_", "").replace("_memory_agent", "").replace("_agent", "")
+        result[short] = agent.id
+    return result
+
+
+# -----------------------------------------------------------------
+# System prompt is stored on the agent, not as a message row
+# -----------------------------------------------------------------
+
+
+@pytest.mark.asyncio(loop_scope="module")
+async def test_system_prompt_stored_on_agent_not_as_message(msg_client):
+    """The system prompt lives in agent_state.system. Updating it should
+    never create a message row with role='system' in the messages table.
+    """
+    client = msg_client
+    agent_map = await _get_sub_agent_ids(client)
+
+    agent_name = "episodic"
+    if agent_name not in agent_map:
+        pytest.skip(f"Agent '{agent_name}' not found")
+
+    agent_id = agent_map[agent_name]
+
+    new_prompt = (
+        "You are an episodic memory agent for integration testing. " "Extract episodic events from conversations."
+    )
+    updated = await client.update_system_prompt(agent_name=agent_name, system_prompt=new_prompt)
+
+    assert updated.system == new_prompt
+
+    await asyncio.sleep(1)
+
+    messages = await _get_message_rows(
+        agent_id=agent_id,
+        user_id=MSG_TEST_USER_ID,
+        org_id=TEST_ORG_ID,
+    )
+    system_msgs = [m for m in messages if m.role == "system"]
+    assert len(system_msgs) == 0, (
+        f"System prompt should not be stored as a message row; " f"found {len(system_msgs)} system message(s)"
+    )
+
+
+# -----------------------------------------------------------------
+# Retention=0: no message rows persist after processing
+# -----------------------------------------------------------------
+
+
+@pytest.mark.asyncio(loop_scope="module")
+async def test_no_messages_persisted_with_zero_retention(msg_client):
+    """When a client has message_set_retention_count=0, processing a
+    conversation should leave zero message rows in the DB for every
+    agent in the pipeline.
+    """
+    client = msg_client
+    agent_map = await _get_sub_agent_ids(client)
+
+    server = _get_server()
+    db_client = await server.client_manager.get_client_by_id(MSG_TEST_CLIENT_ID)
+    assert (db_client.message_set_retention_count or 0) == 0, "Test client should default to retention=0"
+
+    result = await client.add(
+        user_id=MSG_TEST_USER_ID,
+        messages=[
+            {
+                "role": "user",
+                "content": [
+                    {
+                        "type": "text",
+                        "text": "I had lunch with Alex at the Italian place on 5th Ave.",
+                    }
+                ],
+            },
+            {
+                "role": "assistant",
+                "content": [
+                    {
+                        "type": "text",
+                        "text": "Got it, I'll remember your lunch with Alex.",
+                    }
+                ],
+            },
+        ],
+    )
+    assert result.get("success") is True
+
+    print("  Waiting for queue processing (15s)...")
+    await asyncio.sleep(15)
+
+    synthetic_markers = [
+        "[System Message] As the meta memory manager",
+        "continue chaining",
+        "function failed",
+        "finish_memory_update",
+    ]
+
+    for name, aid in agent_map.items():
+        messages = await _get_message_rows(
+            agent_id=aid,
+            user_id=MSG_TEST_USER_ID,
+            org_id=TEST_ORG_ID,
+        )
+        for message in messages:
+            content_text = " ".join([c.text for c in (message.content or []) if hasattr(c, "text") and c.text])
+            assert not any(marker in content_text for marker in synthetic_markers), (
+                f"Agent '{name}' persisted synthetic helper content with retention=0: " f"{content_text}"
+            )
+        assert len(messages) == 0, (
+            f"Agent '{name}' should have 0 message rows with " f"retention=0, found {len(messages)}"
+        )
+
+
+# -----------------------------------------------------------------
+# Retention=N: keeps at most N message-sets, prunes older ones
+# -----------------------------------------------------------------
+
+
+@pytest.mark.asyncio(loop_scope="module")
+async def test_message_retention_prunes_to_limit(msg_client):
+    """With message_set_retention_count=2, sending 3 conversations should
+    leave at most 2 retained message rows for the meta agent. The oldest
+    message-set is pruned after each save.
+    """
+    client = msg_client
+    agent_map = await _get_sub_agent_ids(client)
+
+    if "meta_memory_agent" not in agent_map:
+        pytest.skip("Meta agent not found")
+
+    meta_agent_id = agent_map["meta_memory_agent"]
+
+    server = _get_server()
+    from mirix.schemas.client import ClientUpdate
+
+    updated_client = await server.client_manager.update_client(
+        ClientUpdate(id=MSG_TEST_CLIENT_ID, message_set_retention_count=2)
+    )
+    assert updated_client.message_set_retention_count == 2
+
+    try:
+        conversations = [
+            "I went hiking at Mount Tamalpais this morning.",
+            "I finished reading The Great Gatsby last night.",
+            "I started learning to play guitar today.",
+        ]
+
+        for i, text in enumerate(conversations):
+            result = await client.add(
+                user_id=MSG_TEST_USER_ID,
+                messages=[
+                    {
+                        "role": "user",
+                        "content": [{"type": "text", "text": text}],
+                    },
+                    {
+                        "role": "assistant",
+                        "content": [
+                            {
+                                "type": "text",
+                                "text": f"Noted. (conversation {i+1})",
+                            }
+                        ],
+                    },
+                ],
+            )
+            assert result.get("success") is True
+
+            print(f"  Sent conversation {i+1}/3, waiting 15s...")
+            await asyncio.sleep(15)
+
+        messages = await _get_message_rows(
+            agent_id=meta_agent_id,
+            user_id=MSG_TEST_USER_ID,
+            org_id=TEST_ORG_ID,
+        )
+
+        assert len(messages) <= 2, (
+            f"Expected at most 2 retained message rows with " f"retention=2, found {len(messages)}"
+        )
+
+        synthetic_markers = [
+            "[System Message] As the meta memory manager",
+            "continue chaining",
+            "function failed",
+            "finish_memory_update",
+        ]
+        for message in messages:
+            content_text = " ".join([c.text for c in (message.content or []) if hasattr(c, "text") and c.text])
+            assert not any(marker in content_text for marker in synthetic_markers), (
+                "Retention rows should contain only persisted input message sets, "
+                f"found synthetic helper content: {content_text}"
+            )
+
+        # Sub-agents should not persist retained input message sets.
+        for name, aid in agent_map.items():
+            if name == "meta_memory_agent":
+                continue
+            sub_messages = await _get_message_rows(
+                agent_id=aid,
+                user_id=MSG_TEST_USER_ID,
+                org_id=TEST_ORG_ID,
+            )
+            assert len(sub_messages) == 0, (
+                f"Sub-agent '{name}' should not persist retained message rows; " f"found {len(sub_messages)}"
+            )
+
+    finally:
+        reset_client = await server.client_manager.update_client(
+            ClientUpdate(id=MSG_TEST_CLIENT_ID, message_set_retention_count=0)
+        )
+        assert (reset_client.message_set_retention_count or 0) == 0
+
+        from mirix.services.message_manager import MessageManager
+
+        mm = MessageManager()
+        await mm.hard_delete_user_messages_for_agent(
+            agent_id=meta_agent_id,
+            user_id=MSG_TEST_USER_ID,
+            actor=reset_client,
+            keep_newest_n=0,
+        )
+
+
+# -----------------------------------------------------------------
+# Failed processing leaves no partial message state
+# -----------------------------------------------------------------
+
+
+@pytest.mark.asyncio(loop_scope="module")
+async def test_failed_processing_leaves_no_messages(msg_client):
+    """When processing fails (e.g. input exceeds the context window),
+    no partial message rows should remain in the DB.
+    """
+    client = msg_client
+    agent_map = await _get_sub_agent_ids(client)
+
+    if "meta_memory_agent" not in agent_map:
+        pytest.skip("Meta agent not found")
+
+    server = _get_server()
+    db_client = await server.client_manager.get_client_by_id(MSG_TEST_CLIENT_ID)
+    assert (db_client.message_set_retention_count or 0) == 0
+
+    # ~2M chars / ~500k tokens — well beyond any model's context window
+    huge_text = "overflow " * 200_000
+
+    try:
+        await client.add(
+            user_id=MSG_TEST_USER_ID,
+            messages=[
+                {
+                    "role": "user",
+                    "content": [{"type": "text", "text": huge_text}],
+                },
+                {
+                    "role": "assistant",
+                    "content": [{"type": "text", "text": "Acknowledged."}],
+                },
+            ],
+        )
+    except Exception:
+        pass
+
+    print("  Waiting for processing attempt (20s)...")
+    await asyncio.sleep(20)
+
+    for name, aid in agent_map.items():
+        messages = await _get_message_rows(
+            agent_id=aid,
+            user_id=MSG_TEST_USER_ID,
+            org_id=TEST_ORG_ID,
+        )
+        assert len(messages) == 0, (
+            f"Agent '{name}' should have 0 message rows after a " f"failed processing attempt, found {len(messages)}"
+        )
+
+
 if __name__ == "__main__":
     pytest.main([__file__, "-v", "-s", "-m", "integration"])
diff --git a/tests/test_memory_server.py b/tests/test_memory_server.py
index c5819bc96..54cdabcbd 100644
--- a/tests/test_memory_server.py
+++ b/tests/test_memory_server.py
@@ -719,11 +719,21 @@ async def test_trigger_memory_update_runs_in_parallel(self, server, client, user
         relevant_agents = [agent for agent in child_agents if agent.agent_type in target_types]
         assert len(relevant_agents) == len(target_types), "Expected episodic and procedural memory agents to be present"
 
-        tracker = {"start_times": {}, "thread_ids": {}}
+        tracker = {"start_times": {}, "thread_ids": {}, "input_lengths": {}}
         lock = threading.Lock()
 
         class MockMemoryAgent:
-            def __init__(self, agent_state, interface, actor, user, filter_tags=None, block_filter_tags=None, use_cache=True, **kwargs):
+            def __init__(
+                self,
+                agent_state,
+                interface,
+                actor,
+                user,
+                filter_tags=None,
+                block_filter_tags=None,
+                use_cache=True,
+                **kwargs,
+            ):
                 self.agent_state = agent_state
 
             async def step(self, input_messages, chaining, actor=None, user=None, topics=None, retrieved_memories=None):
@@ -731,11 +741,13 @@ async def step(self, input_messages, chaining, actor=None, user=None, topics=Non
                 with lock:
                     tracker["start_times"][memory_type] = time.perf_counter()
                     tracker["thread_ids"][memory_type] = threading.get_ident()
+                    tracker["input_lengths"][memory_type] = (
+                        len(input_messages) if isinstance(input_messages, list) else 1
+                    )
                 await asyncio.sleep(1)
 
         monkeypatch.setattr("mirix.agent.EpisodicMemoryAgent", MockMemoryAgent)
         monkeypatch.setattr("mirix.agent.ProceduralMemoryAgent", MockMemoryAgent)
-        monkeypatch.setattr("mirix.functions.function_sets.memory_tools.os.cpu_count", lambda: 8)
 
         class StubAgentManager:
             async def list_agents(self, *, parent_id, actor, limit=None, **kwargs):
@@ -768,6 +780,9 @@ async def list_agents(self, *, parent_id, actor, limit=None, **kwargs):
         assert set(start_times.keys()) == {"episodic", "procedural"}
         gap = abs(start_times["episodic"] - start_times["procedural"])
 
+        # Child agents should receive a single packed input message.
+        assert tracker["input_lengths"] == {"episodic": 1, "procedural": 1}
+
         # Both updates ran; gap < 0.45s indicates concurrent execution (asyncio uses one thread).
         assert gap < 0.45, f"Expected parallel execution, gap was {gap:.3f}s"
 
diff --git a/tests/test_message_handling.py b/tests/test_message_handling.py
index eb8a9c0b3..b119e32bc 100644
--- a/tests/test_message_handling.py
+++ b/tests/test_message_handling.py
@@ -1,27 +1,38 @@
 """
-Tests for message handling, particularly the race condition fix.
+Tests for message handling after the message_ids refactor.
 
 Tests cover:
-1. get_messages_by_ids gracefully handles missing message IDs
-2. get_in_context_messages filters by user when user is provided
-3. get_in_context_messages returns all messages when user is not provided
+1. get_messages_for_agent_user returns messages in chronological order
+2. hard_delete_user_messages_for_agent deletes correct rows and keeps newest N
+3. Retention=0 path: no DB persistence after step
+4. Retention=N path: persists input messages and prunes to N newest
+5. Context overflow summarization recovery
 """
 
+import asyncio
 from contextlib import asynccontextmanager
 from datetime import datetime
+from types import SimpleNamespace
 from unittest.mock import AsyncMock, MagicMock, patch
 
+import httpx
 import pytest
 
-from mirix.schemas.agent import AgentState
+from mirix.agent.agent import Agent
+from mirix.errors import ContextWindowExceededError
+from mirix.schemas.agent import AgentState, AgentStepResponse, AgentType
 from mirix.schemas.client import Client
+from mirix.schemas.embedding_config import EmbeddingConfig
+from mirix.schemas.enums import MessageRole
+from mirix.schemas.llm_config import LLMConfig
 from mirix.schemas.message import Message
+from mirix.schemas.mirix_message_content import TextContent
+from mirix.schemas.openai.chat_completion_response import UsageStatistics
 from mirix.schemas.user import User
-from mirix.services.agent_manager import AgentManager
 from mirix.services.message_manager import MessageManager
 
 
-def make_client(id="client-1", org_id="org-1"):
+def make_client(id="client-1", org_id="org-1", retention=0):
     """Create a real Client object for tests."""
     return Client(
         id=id,
@@ -30,6 +41,7 @@ def make_client(id="client-1", org_id="org-1"):
         status="active",
         write_scope="test",
         read_scopes=["test"],
+        message_set_retention_count=retention,
         created_at=datetime.now(),
         updated_at=datetime.now(),
         is_deleted=False,
@@ -50,196 +62,635 @@ def make_user(id="user-1", org_id="org-1"):
     )
 
 
-def make_agent_state(message_ids=None):
-    """Create a mock AgentState with spec for type checking."""
-    agent_state = MagicMock(spec=AgentState)
-    agent_state.message_ids = message_ids or []
-    return agent_state
+def make_pydantic_message(id: str, role: str = "user", user_id: str = "user-1") -> MagicMock:
+    msg = MagicMock(spec=Message)
+    msg.id = id
+    msg.role = role
+    msg.user_id = user_id
+    return msg
 
 
-@pytest.mark.asyncio
-class TestGetMessagesByIds:
-    """Tests for MessageManager.get_messages_by_ids() - race condition fix"""
+class TestGetMessagesForAgentUser:
+    """Tests for MessageManager.get_messages_for_agent_user()"""
 
-    async def test_returns_existing_messages_skips_missing(self):
-        """
-        Test that get_messages_by_ids returns existing messages and skips missing ones.
-
-        This is the key fix for the race condition - when concurrent workers
-        delete messages via summarization, other workers should not crash.
-        """
+    def test_returns_messages_in_chronological_order(self):
+        """DB returns newest-first; method should reverse to chronological."""
         manager = MessageManager()
 
-        # Mock the session and MessageModel.list to return only 2 of 3 requested messages
-        mock_session = MagicMock()
-        mock_msg1 = MagicMock()
-        mock_msg1.id = "msg-1"
-        mock_msg1.to_pydantic.return_value = MagicMock(id="msg-1")
+        # Simulate DB returning newest-first (DESC order)
+        msg_old = MagicMock()
+        msg_old.to_pydantic.return_value = make_pydantic_message("msg-1")
+        msg_new = MagicMock()
+        msg_new.to_pydantic.return_value = make_pydantic_message("msg-2")
 
-        mock_msg2 = MagicMock()
-        mock_msg2.id = "msg-2"
-        mock_msg2.to_pydantic.return_value = MagicMock(id="msg-2")
+        mock_result = MagicMock()
+        mock_result.scalars.return_value.all.return_value = [msg_new, msg_old]  # newest first from DB
 
-        # msg-3 is "missing" (simulates deletion by another worker)
+        mock_session = AsyncMock()
+        mock_session.execute = AsyncMock(return_value=mock_result)
 
         @asynccontextmanager
         async def _async_cm():
             yield mock_session
 
-        with patch.object(manager, "session_maker") as mock_session_maker:
-            mock_session_maker.return_value = _async_cm()
-
-            with patch("mirix.services.message_manager.MessageModel") as MockMessageModel:
-                MockMessageModel.list = AsyncMock(return_value=[mock_msg1, mock_msg2])
-
+        async def run():
+            with patch.object(manager, "session_maker", return_value=_async_cm()):
                 actor = make_client()
-
-                # Request 3 messages, but only 2 exist
-                result = await manager.get_messages_by_ids(
-                    message_ids=["msg-1", "msg-2", "msg-3"], actor=actor
+                return await manager.get_messages_for_agent_user(
+                    agent_id="agent-1", user_id="user-1", actor=actor, limit=10
                 )
 
-                # Should return only the 2 that exist, not crash
-                assert len(result) == 2
-                assert result[0].id == "msg-1"
-                assert result[1].id == "msg-2"
+        result = asyncio.run(run())
+
+        # Should be reversed to chronological order
+        assert len(result) == 2
+        assert result[0].id == "msg-1"  # oldest first
+        assert result[1].id == "msg-2"
 
-    async def test_preserves_order_of_existing_messages(self):
-        """Test that returned messages maintain the requested order."""
+    def test_returns_empty_when_no_messages(self):
+        """Returns empty list when no messages exist."""
         manager = MessageManager()
 
-        mock_msg2 = MagicMock()
-        mock_msg2.id = "msg-2"
-        mock_msg2.to_pydantic.return_value = MagicMock(id="msg-2")
+        mock_result = MagicMock()
+        mock_result.scalars.return_value.all.return_value = []
 
-        mock_msg1 = MagicMock()
-        mock_msg1.id = "msg-1"
-        mock_msg1.to_pydantic.return_value = MagicMock(id="msg-1")
+        mock_session = AsyncMock()
+        mock_session.execute = AsyncMock(return_value=mock_result)
 
         @asynccontextmanager
         async def _async_cm():
-            yield MagicMock()
-
-        with patch.object(manager, "session_maker") as mock_session_maker:
-            mock_session_maker.return_value = _async_cm()
-
-            with patch("mirix.services.message_manager.MessageModel") as MockMessageModel:
-                # DB returns in different order
-                MockMessageModel.list = AsyncMock(return_value=[mock_msg2, mock_msg1])
+            yield mock_session
 
+        async def run():
+            with patch.object(manager, "session_maker", return_value=_async_cm()):
                 actor = make_client()
-
-                result = await manager.get_messages_by_ids(
-                    message_ids=["msg-1", "msg-2"], actor=actor
+                return await manager.get_messages_for_agent_user(
+                    agent_id="agent-1", user_id="user-1", actor=actor, limit=10
                 )
 
-                # Should be in requested order, not DB order
-                assert result[0].id == "msg-1"
-                assert result[1].id == "msg-2"
+        result = asyncio.run(run())
+        assert result == []
+
+
+class TestHardDeleteUserMessagesForAgent:
+    """Tests for MessageManager.hard_delete_user_messages_for_agent()"""
 
-    async def test_returns_empty_list_when_all_missing(self):
-        """Test that an empty list is returned when all messages are missing."""
+    def test_deletes_all_when_keep_newest_n_is_zero(self):
+        """keep_newest_n=0 means delete everything."""
         manager = MessageManager()
 
-        @asynccontextmanager
-        async def _async_cm():
-            yield MagicMock()
+        delete_ids_result = MagicMock()
+        delete_ids_result.all.return_value = [("msg-1",), ("msg-2",), ("msg-3",)]
 
-        with patch.object(manager, "session_maker") as mock_session_maker:
-            mock_session_maker.return_value = _async_cm()
+        execute_results = [
+            delete_ids_result,  # select IDs to delete
+            MagicMock(),  # DELETE statement
+        ]
 
-            with patch("mirix.services.message_manager.MessageModel") as MockMessageModel:
-                MockMessageModel.list = AsyncMock(return_value=[])
+        mock_session = AsyncMock()
+        mock_session.execute = AsyncMock(side_effect=execute_results)
+        mock_session.commit = AsyncMock()
 
-                actor = make_client()
+        @asynccontextmanager
+        async def _async_cm():
+            yield mock_session
 
-                result = await manager.get_messages_by_ids(
-                    message_ids=["msg-1", "msg-2"], actor=actor
-                )
+        async def run():
+            with patch.object(manager, "session_maker", return_value=_async_cm()):
+                with patch("mirix.database.redis_client.get_redis_client", return_value=None):
+                    actor = make_client()
+                    return await manager.hard_delete_user_messages_for_agent(
+                        agent_id="agent-1",
+                        user_id="user-1",
+                        actor=actor,
+                        keep_newest_n=0,
+                    )
+
+        count = asyncio.run(run())
+        assert count == 3
+
+    def test_returns_zero_when_no_messages_exist(self):
+        """Returns 0 when there are no messages to delete."""
+        manager = MessageManager()
 
-                assert result == []
+        delete_ids_result = MagicMock()
+        delete_ids_result.all.return_value = []  # nothing to delete
 
+        mock_session = AsyncMock()
+        mock_session.execute = AsyncMock(return_value=delete_ids_result)
+        mock_session.commit = AsyncMock()
 
-@pytest.mark.asyncio
-class TestGetInContextMessages:
-    """Tests for AgentManager.get_in_context_messages() - user filtering fix"""
+        @asynccontextmanager
+        async def _async_cm():
+            yield mock_session
 
-    async def test_filters_by_user_id_when_user_provided(self):
-        """
-        Test that messages are filtered by user.id when user parameter is provided.
+        async def run():
+            with patch.object(manager, "session_maker", return_value=_async_cm()):
+                actor = make_client()
+                return await manager.hard_delete_user_messages_for_agent(
+                    agent_id="agent-1",
+                    user_id="user-1",
+                    actor=actor,
+                    keep_newest_n=0,
+                )
 
-        This fixes the bug where actor.id (client ID) was used instead of user.id.
-        """
-        manager = AgentManager()
+        count = asyncio.run(run())
+        assert count == 0
+
+
+class TestRetentionBehavior:
+    """Tests that retention=0 vs retention>0 produces correct persistence behavior."""
+
+    def test_client_default_retention_is_zero(self):
+        """Clients default to message_set_retention_count=0."""
+        client = make_client()
+        assert (client.message_set_retention_count or 0) == 0
+
+    def test_client_with_retention_has_correct_value(self):
+        """Clients configured with retention=5 expose that value."""
+        client = make_client(retention=5)
+        assert client.message_set_retention_count == 5
+
+
+def make_agent_state(
+    agent_id: str,
+    agent_type: AgentType,
+    parent_id: str | None = None,
+) -> AgentState:
+    """Create a minimal AgentState for unit-testing Agent.step."""
+    return AgentState(
+        id=agent_id,
+        name=agent_type.value,
+        system="System prompt",
+        agent_type=agent_type,
+        llm_config=LLMConfig.default_config("gpt-4o-mini"),
+        embedding_config=EmbeddingConfig.default_config(provider="openai"),
+        tools=[],
+        parent_id=parent_id,
+    )
 
-        # Create mock messages
-        system_msg = MagicMock()
-        system_msg.user_id = "system"
 
-        user_a_msg = MagicMock()
-        user_a_msg.user_id = "user-a"
+def make_runtime_message(agent_id: str, text: str) -> Message:
+    """Create a runtime Message object used by Agent.step."""
+    return Message.dict_to_message(
+        agent_id=agent_id,
+        model="gpt-4o-mini",
+        openai_message_dict={"role": "user", "content": text},
+    )
 
-        user_b_msg = MagicMock()
-        user_b_msg.user_id = "user-b"
 
-        with patch.object(manager, "message_manager") as mock_msg_manager:
-            mock_msg_manager.get_messages_by_ids = AsyncMock(
-                return_value=[system_msg, user_a_msg, user_b_msg]
+def build_step_test_agent(agent_state: AgentState, user: User) -> Agent:
+    """Build an Agent instance with only fields required by step()."""
+    agent = Agent.__new__(Agent)
+    agent.agent_state = agent_state
+    agent.user = user
+    agent.user_id = user.id
+    agent.client_id = "client-1"
+    agent.model = "gpt-4o-mini"
+    agent.filter_tags = None
+    agent.block_filter_tags = None
+    agent._block_scopes = None
+    agent.blocks_in_memory = None
+    agent.last_function_response = None
+    agent.block_manager = SimpleNamespace(get_blocks=AsyncMock(return_value=[]))
+    agent.message_manager = SimpleNamespace(
+        get_messages_for_agent_user=AsyncMock(return_value=[]),
+        create_many_messages=AsyncMock(return_value=[]),
+        hard_delete_user_messages_for_agent=AsyncMock(return_value=0),
+    )
+    agent._extract_topics_from_messages = AsyncMock(return_value="topic-a;topic-b")
+    agent.inner_step = AsyncMock(
+        return_value=AgentStepResponse(
+            messages=[],
+            continue_chaining=False,
+            function_failed=False,
+            usage=UsageStatistics(),
+            traj={},
+        )
+    )
+    agent.interface = SimpleNamespace(step_complete=lambda: None)
+    return agent
+
+
+class TestAgentStepRetentionAndTopics:
+    @pytest.mark.asyncio
+    async def test_step_reads_retention_from_parent_scope_for_sub_agent(self):
+        user = make_user()
+        client = make_client(retention=2)
+        agent_state = make_agent_state(
+            agent_id="agent-child",
+            agent_type=AgentType.episodic_memory_agent,
+            parent_id="agent-meta",
+        )
+        agent = build_step_test_agent(agent_state, user)
+        agent.message_manager.get_messages_for_agent_user = AsyncMock(
+            return_value=[make_runtime_message("agent-meta", "r1")]
+        )
+
+        with patch("mirix.agent.agent.LLMClient.create", return_value=object()):
+            await agent.step(
+                input_messages=make_runtime_message("agent-child", "current"),
+                chaining=False,
+                actor=client,
+                user=user,
             )
 
-            agent_state = make_agent_state(message_ids=["sys-1", "msg-a", "msg-b"])
-            actor = make_client(id="client-123")
-            user = make_user(id="user-a")  # Should filter to this user's messages
-
-            result = await manager.get_in_context_messages(
-                agent_state=agent_state, actor=actor, user=user
+        agent.message_manager.get_messages_for_agent_user.assert_awaited_once()
+        read_kwargs = agent.message_manager.get_messages_for_agent_user.await_args.kwargs
+        assert read_kwargs["agent_id"] == "agent-meta"
+        assert read_kwargs["limit"] == 2
+        agent.message_manager.create_many_messages.assert_not_awaited()
+        agent.message_manager.hard_delete_user_messages_for_agent.assert_not_awaited()
+        agent._extract_topics_from_messages.assert_not_awaited()
+
+    @pytest.mark.asyncio
+    async def test_step_meta_persists_only_original_input_and_prunes(self):
+        user = make_user()
+        client = make_client(retention=2)
+        agent_state = make_agent_state(
+            agent_id="agent-meta",
+            agent_type=AgentType.meta_memory_agent,
+        )
+        agent = build_step_test_agent(agent_state, user)
+        original_input = make_runtime_message("agent-meta", "persist-me")
+        heartbeat_like_message = make_runtime_message("agent-meta", "heartbeat-ish follow-up")
+        agent.inner_step = AsyncMock(
+            return_value=AgentStepResponse(
+                messages=[heartbeat_like_message],
+                continue_chaining=False,
+                function_failed=False,
+                usage=UsageStatistics(),
+                traj={},
+            )
+        )
+
+        with patch("mirix.agent.agent.LLMClient.create", return_value=object()):
+            await agent.step(
+                input_messages=original_input,
+                chaining=False,
+                actor=client,
+                user=user,
             )
 
-            # Should have system message + only user-a's message
-            assert len(result) == 2
-            assert result[0] == system_msg
-            assert result[1] == user_a_msg
+        persisted_messages = agent.message_manager.create_many_messages.await_args.args[0]
+        assert len(persisted_messages) == 1
+        assert persisted_messages[0].id == original_input.id
+
+        prune_kwargs = agent.message_manager.hard_delete_user_messages_for_agent.await_args.kwargs
+        assert prune_kwargs["agent_id"] == "agent-meta"
+        assert prune_kwargs["keep_newest_n"] == 2
+
+    @pytest.mark.asyncio
+    async def test_step_meta_extracts_topics_from_retained_plus_current(self):
+        user = make_user()
+        client = make_client(retention=2)
+        agent_state = make_agent_state(
+            agent_id="agent-meta",
+            agent_type=AgentType.meta_memory_agent,
+        )
+        agent = build_step_test_agent(agent_state, user)
+        retained_1 = make_runtime_message("agent-meta", "retained-one")
+        retained_2 = make_runtime_message("agent-meta", "retained-two")
+        current = make_runtime_message("agent-meta", "current-input")
+        agent.message_manager.get_messages_for_agent_user = AsyncMock(return_value=[retained_1, retained_2])
+
+        with patch("mirix.agent.agent.LLMClient.create", return_value=object()):
+            await agent.step(
+                input_messages=current,
+                chaining=False,
+                actor=client,
+                user=user,
+            )
 
-    async def test_no_filtering_when_user_not_provided(self):
-        """
-        Test that all messages are returned when user parameter is not provided.
+        extract_arg = agent._extract_topics_from_messages.await_args.args[0]
+        assert [m.id for m in extract_arg] == [retained_1.id, retained_2.id, current.id]
+
+    @pytest.mark.asyncio
+    async def test_step_retention_zero_skips_read_write_persistence(self):
+        user = make_user()
+        client = make_client(retention=0)
+        agent_state = make_agent_state(
+            agent_id="agent-meta",
+            agent_type=AgentType.meta_memory_agent,
+        )
+        agent = build_step_test_agent(agent_state, user)
+
+        with patch("mirix.agent.agent.LLMClient.create", return_value=object()):
+            await agent.step(
+                input_messages=make_runtime_message("agent-meta", "current-input"),
+                chaining=False,
+                actor=client,
+                user=user,
+            )
 
-        This maintains backward compatibility.
-        """
-        manager = AgentManager()
+        agent.message_manager.get_messages_for_agent_user.assert_not_awaited()
+        agent.message_manager.create_many_messages.assert_not_awaited()
+        agent.message_manager.hard_delete_user_messages_for_agent.assert_not_awaited()
+
+
+def _make_context_overflow_error():
+    """Create an httpx error that is_context_overflow_error() recognises."""
+    request = httpx.Request("POST", "https://api.openai.com/v1/chat/completions")
+    response = httpx.Response(
+        400,
+        json={
+            "error": {
+                "message": "This model's maximum context length is 8192 tokens",
+                "type": "invalid_request_error",
+                "code": "context_length_exceeded",
+            }
+        },
+        request=request,
+    )
+    return httpx.HTTPStatusError(
+        message="maximum context length",
+        request=request,
+        response=response,
+    )
 
-        system_msg = MagicMock()
-        user_a_msg = MagicMock()
-        user_b_msg = MagicMock()
 
-        with patch.object(manager, "message_manager") as mock_msg_manager:
-            mock_msg_manager.get_messages_by_ids = AsyncMock(
-                return_value=[system_msg, user_a_msg, user_b_msg]
+def build_inner_step_test_agent(agent_state: AgentState, user: User) -> Agent:
+    """Build an Agent with mocks suitable for testing inner_step directly."""
+    agent = Agent.__new__(Agent)
+    agent.agent_state = agent_state
+    agent.user = user
+    agent.user_id = user.id
+    agent.client_id = "client-1"
+    agent.model = "gpt-4o-mini"
+    agent.filter_tags = None
+    agent.block_filter_tags = None
+    agent._block_scopes = None
+    agent.blocks_in_memory = None
+    agent.last_function_response = None
+    agent.logger = MagicMock()
+    agent.block_manager = SimpleNamespace(get_blocks=AsyncMock(return_value=[]))
+    agent.message_manager = SimpleNamespace(
+        get_messages_for_agent_user=AsyncMock(return_value=[]),
+        create_many_messages=AsyncMock(return_value=[]),
+        hard_delete_user_messages_for_agent=AsyncMock(return_value=0),
+        create_message=AsyncMock(side_effect=lambda msg, **kw: msg),
+        delete_message_by_id=AsyncMock(),
+    )
+    agent.step_manager = SimpleNamespace(
+        log_step=AsyncMock(return_value=SimpleNamespace(id="step-1")),
+    )
+    agent.interface = SimpleNamespace(step_complete=lambda: None)
+    agent.actor = make_client(retention=3)
+    return agent
+
+
+class TestSummarizeAndReplaceRetainedMessages:
+    """Tests for Agent.summarize_and_replace_retained_messages()"""
+
+    @pytest.mark.asyncio
+    async def test_calls_summarize_and_persists_summary(self):
+        """Verifies the method calls summarize_messages, persists the result,
+        and deletes the original retained messages."""
+        user = make_user()
+        agent_state = make_agent_state("agent-1", AgentType.meta_memory_agent)
+        agent = build_inner_step_test_agent(agent_state, user)
+
+        retained = [
+            make_runtime_message("agent-1", "old-msg-1"),
+            make_runtime_message("agent-1", "old-msg-2"),
+        ]
+
+        with patch("mirix.agent.agent.summarize_messages", new_callable=AsyncMock) as mock_summarize:
+            mock_summarize.return_value = "Summary of old messages"
+            result = await agent.summarize_and_replace_retained_messages(retained)
+
+        mock_summarize.assert_awaited_once()
+        assert result.message_type == "summary"
+        assert result.role == MessageRole.user
+        assert result.content[0].text == "Summary of old messages"
+
+        agent.message_manager.create_message.assert_awaited_once()
+        assert agent.message_manager.delete_message_by_id.await_count == 2
+
+    @pytest.mark.asyncio
+    async def test_summary_message_has_correct_agent_and_user(self):
+        """Summary message should be scoped to the correct agent and user."""
+        user = make_user()
+        agent_state = make_agent_state("agent-1", AgentType.meta_memory_agent)
+        agent = build_inner_step_test_agent(agent_state, user)
+
+        retained = [make_runtime_message("agent-1", "old-msg")]
+
+        with patch("mirix.agent.agent.summarize_messages", new_callable=AsyncMock) as mock_summarize:
+            mock_summarize.return_value = "Summary"
+            result = await agent.summarize_and_replace_retained_messages(retained)
+
+        assert result.agent_id == "agent-1"
+        assert result.user_id == "user-1"
+
+    @pytest.mark.asyncio
+    async def test_summary_scoped_to_meta_agent_when_called_from_sub_agent(self):
+        """When a sub-agent summarizes, the summary message's agent_id should
+        be the parent (meta) agent, not the sub-agent itself."""
+        user = make_user()
+        agent_state = make_agent_state(
+            "agent-child",
+            AgentType.episodic_memory_agent,
+            parent_id="agent-meta",
+        )
+        agent = build_inner_step_test_agent(agent_state, user)
+
+        retained = [make_runtime_message("agent-meta", "old-msg")]
+
+        with patch("mirix.agent.agent.summarize_messages", new_callable=AsyncMock) as mock_summarize:
+            mock_summarize.return_value = "Summary"
+            result = await agent.summarize_and_replace_retained_messages(retained)
+
+        assert result.agent_id == "agent-meta"
+        assert result.user_id == "user-1"
+
+
+class TestContextOverflowSummarizationRecovery:
+    """Tests for the summarization recovery path in inner_step."""
+
+    @pytest.mark.asyncio
+    async def test_summarization_triggered_on_overflow_with_retained_messages(self):
+        """When context overflows and retained messages exist, summarization
+        should be attempted and inner_step retried."""
+        user = make_user()
+        agent_state = make_agent_state("agent-1", AgentType.meta_memory_agent)
+        agent = build_inner_step_test_agent(agent_state, user)
+
+        retained_msg = make_runtime_message("agent-1", "retained")
+        current_msg = make_runtime_message("agent-1", "current")
+        summary_msg = Message(
+            agent_id="agent-1",
+            role=MessageRole.user,
+            content=[TextContent(text="Summary")],
+            message_type="summary",
+        )
+
+        call_count = 0
+
+        async def mock_get_ai_reply(*args, **kwargs):
+            nonlocal call_count
+            call_count += 1
+            if call_count == 1:
+                raise _make_context_overflow_error()
+            # Second call succeeds
+            return MagicMock(
+                choices=[MagicMock(message=MagicMock(content="ok", tool_calls=None))],
+                usage=UsageStatistics(),
+                id="resp-1",
             )
 
-            agent_state = make_agent_state(message_ids=["sys-1", "msg-a", "msg-b"])
-            actor = make_client()
-
-            # No user parameter
-            result = await manager.get_in_context_messages(
-                agent_state=agent_state, actor=actor
+        agent._get_ai_reply = mock_get_ai_reply
+        agent.build_system_prompt_with_memories = AsyncMock(return_value=("system prompt", {}))
+        agent.summarize_and_replace_retained_messages = AsyncMock(return_value=summary_msg)
+        agent._handle_ai_response = AsyncMock(return_value=([], False, False))
+
+        result = await agent.inner_step(
+            messages=[current_msg],
+            accumulated=[retained_msg],
+            retained_count=1,
+            chaining=False,
+        )
+
+        agent.summarize_and_replace_retained_messages.assert_awaited_once_with([retained_msg], None)
+        assert result is not None
+
+    @pytest.mark.asyncio
+    async def test_hard_fail_when_no_retained_messages(self):
+        """When context overflows but there are no retained messages,
+        ContextWindowExceededError should be raised immediately."""
+        user = make_user()
+        agent_state = make_agent_state("agent-1", AgentType.meta_memory_agent)
+        agent = build_inner_step_test_agent(agent_state, user)
+
+        current_msg = make_runtime_message("agent-1", "current")
+
+        agent._get_ai_reply = AsyncMock(side_effect=_make_context_overflow_error())
+        agent.build_system_prompt_with_memories = AsyncMock(return_value=("system prompt", {}))
+
+        with pytest.raises(ContextWindowExceededError):
+            await agent.inner_step(
+                messages=[current_msg],
+                accumulated=[],
+                retained_count=0,
+                chaining=False,
             )
 
-            # Should return all messages (no filtering)
-            assert len(result) == 3
-
-    async def test_returns_empty_when_no_messages(self):
-        """Test that empty list is returned when agent has no messages."""
-        manager = AgentManager()
-
-        with patch.object(manager, "message_manager") as mock_msg_manager:
-            mock_msg_manager.get_messages_by_ids = AsyncMock(return_value=[])
+    @pytest.mark.asyncio
+    async def test_hard_fail_after_summarization_already_attempted(self):
+        """If summarization was already attempted and context still overflows,
+        raise ContextWindowExceededError."""
+        user = make_user()
+        agent_state = make_agent_state("agent-1", AgentType.meta_memory_agent)
+        agent = build_inner_step_test_agent(agent_state, user)
+
+        summary_msg = Message(
+            agent_id="agent-1",
+            role=MessageRole.user,
+            content=[TextContent(text="Summary")],
+            message_type="summary",
+        )
+        current_msg = make_runtime_message("agent-1", "current")
+
+        agent._get_ai_reply = AsyncMock(side_effect=_make_context_overflow_error())
+        agent.build_system_prompt_with_memories = AsyncMock(return_value=("system prompt", {}))
+
+        with pytest.raises(ContextWindowExceededError):
+            await agent.inner_step(
+                messages=[current_msg],
+                accumulated=[summary_msg],
+                retained_count=1,
+                _summarization_attempted=True,
+                chaining=False,
+            )
 
-            agent_state = make_agent_state(message_ids=[])
-            actor = make_client()
+    @pytest.mark.asyncio
+    async def test_hard_fail_when_summarization_itself_fails(self):
+        """If summarize_and_replace_retained_messages raises, the original
+        context overflow should still surface as ContextWindowExceededError."""
+        user = make_user()
+        agent_state = make_agent_state("agent-1", AgentType.meta_memory_agent)
+        agent = build_inner_step_test_agent(agent_state, user)
+
+        retained_msg = make_runtime_message("agent-1", "retained")
+        current_msg = make_runtime_message("agent-1", "current")
+
+        agent._get_ai_reply = AsyncMock(side_effect=_make_context_overflow_error())
+        agent.build_system_prompt_with_memories = AsyncMock(return_value=("system prompt", {}))
+        agent.summarize_and_replace_retained_messages = AsyncMock(side_effect=RuntimeError("LLM summarization failed"))
+
+        with pytest.raises(ContextWindowExceededError, match="summarization recovery failed"):
+            await agent.inner_step(
+                messages=[current_msg],
+                accumulated=[retained_msg],
+                retained_count=1,
+                chaining=False,
+            )
 
-            result = await manager.get_in_context_messages(
-                agent_state=agent_state, actor=actor
+    @pytest.mark.asyncio
+    async def test_chaining_outputs_preserved_after_summarization(self):
+        """When summarization fires, chaining outputs (accumulated beyond
+        retained_count) should be preserved in the retry."""
+        user = make_user()
+        agent_state = make_agent_state("agent-1", AgentType.meta_memory_agent)
+        agent = build_inner_step_test_agent(agent_state, user)
+
+        retained_msg = make_runtime_message("agent-1", "retained")
+        chaining_msg = make_runtime_message("agent-1", "heartbeat")
+        current_msg = make_runtime_message("agent-1", "current")
+        summary_msg = Message(
+            agent_id="agent-1",
+            role=MessageRole.user,
+            content=[TextContent(text="Summary")],
+            message_type="summary",
+        )
+
+        call_count = 0
+
+        async def mock_get_ai_reply(*args, **kwargs):
+            nonlocal call_count
+            call_count += 1
+            if call_count == 1:
+                raise _make_context_overflow_error()
+            return MagicMock(
+                choices=[MagicMock(message=MagicMock(content="ok", tool_calls=None))],
+                usage=UsageStatistics(),
+                id="resp-1",
             )
 
-            assert result == []
+        agent._get_ai_reply = mock_get_ai_reply
+        agent.build_system_prompt_with_memories = AsyncMock(return_value=("system prompt", {}))
+        agent.summarize_and_replace_retained_messages = AsyncMock(return_value=summary_msg)
+        agent._handle_ai_response = AsyncMock(return_value=([], False, False))
+
+        result = await agent.inner_step(
+            messages=[current_msg],
+            accumulated=[retained_msg, chaining_msg],
+            retained_count=1,
+            chaining=False,
+        )
+
+        assert result is not None
+        # The retry should have been called with accumulated=[summary_msg, chaining_msg]
+        # and retained_count=1 (for the single summary message)
+        assert call_count == 2
+
+
+class TestMessageTypeField:
+    """Tests for the message_type field on Message schema."""
+
+    def test_default_message_type_is_original(self):
+        msg = Message(
+            agent_id="agent-1",
+            role=MessageRole.user,
+            content=[TextContent(text="hello")],
+        )
+        assert msg.message_type == "original"
+
+    def test_summary_message_type(self):
+        msg = Message(
+            agent_id="agent-1",
+            role=MessageRole.user,
+            content=[TextContent(text="summary text")],
+            message_type="summary",
+        )
+        assert msg.message_type == "summary"
diff --git a/tests/test_multi_scope_access.py b/tests/test_multi_scope_access.py
index 6a87a3b82..c03e2c2d4 100644
--- a/tests/test_multi_scope_access.py
+++ b/tests/test_multi_scope_access.py
@@ -51,9 +51,7 @@ async def test_org():
     try:
         return await org_mgr.get_organization_by_id(org_id)
     except Exception:
-        return await org_mgr.create_organization(
-            PydanticOrganization(id=org_id, name="Multi-Scope Test Org")
-        )
+        return await org_mgr.create_organization(PydanticOrganization(id=org_id, name="Multi-Scope Test Org"))
 
 
 @pytest_asyncio.fixture(scope="module", loop_scope="module")
@@ -206,9 +204,7 @@ async def no_access_client(test_org, client_manager):
 class TestReadOnlyClient:
     """Tests for clients with write_scope=None."""
 
-    async def test_read_only_client_cannot_create_memory(
-        self, raw_memory_manager, read_only_client, test_user
-    ):
+    async def test_read_only_client_cannot_create_memory(self, raw_memory_manager, read_only_client, test_user):
         """Test that a read-only client (write_scope=None) cannot create memories."""
         memory_data = RawMemoryItemCreate(
             context="Attempting to create from read-only client",
@@ -249,9 +245,7 @@ async def test_read_only_client_can_read_from_read_scopes(
             assert created.filter_tags["scope"] == "shared"
 
             # Read-only client should be able to read it (has 'shared' in read_scopes)
-            fetched = await raw_memory_manager.get_raw_memory_by_id(
-                created.id, actor=read_only_client
-            )
+            fetched = await raw_memory_manager.get_raw_memory_by_id(created.id, actor=read_only_client)
             assert fetched.id == created.id
             assert fetched.context == memory_data.context
         finally:
@@ -304,14 +298,10 @@ async def test_client_can_read_from_multiple_scopes(
 
             # multi_read_client has read_scopes=["shared", "private", "multi-read-scope"]
             # It should be able to read both memories
-            fetched_shared = await raw_memory_manager.get_raw_memory_by_id(
-                shared_memory.id, actor=multi_read_client
-            )
+            fetched_shared = await raw_memory_manager.get_raw_memory_by_id(shared_memory.id, actor=multi_read_client)
             assert fetched_shared.id == shared_memory.id
 
-            fetched_private = await raw_memory_manager.get_raw_memory_by_id(
-                private_memory.id, actor=multi_read_client
-            )
+            fetched_private = await raw_memory_manager.get_raw_memory_by_id(private_memory.id, actor=multi_read_client)
             assert fetched_private.id == private_memory.id
         finally:
             # Cleanup
@@ -400,9 +390,7 @@ async def test_writer_creates_reader_reads(
             assert memory.filter_tags["scope"] == "shared"
 
             # Reader can read it
-            fetched = await raw_memory_manager.get_raw_memory_by_id(
-                memory.id, actor=read_only_client
-            )
+            fetched = await raw_memory_manager.get_raw_memory_by_id(memory.id, actor=read_only_client)
             assert fetched.id == memory.id
         finally:
             await raw_memory_manager.delete_raw_memory(memory.id, shared_writer_client)
@@ -480,15 +468,11 @@ async def test_private_client_reads_shared_and_private(
 
         try:
             # Private client can read shared memory
-            fetched_shared = await raw_memory_manager.get_raw_memory_by_id(
-                shared_memory.id, actor=private_client
-            )
+            fetched_shared = await raw_memory_manager.get_raw_memory_by_id(shared_memory.id, actor=private_client)
             assert fetched_shared.id == shared_memory.id
 
             # Private client can read its own private memory
-            fetched_private = await raw_memory_manager.get_raw_memory_by_id(
-                private_memory.id, actor=private_client
-            )
+            fetched_private = await raw_memory_manager.get_raw_memory_by_id(private_memory.id, actor=private_client)
             assert fetched_private.id == private_memory.id
         finally:
             await raw_memory_manager.delete_raw_memory(shared_memory.id, shared_writer_client)
@@ -527,9 +511,7 @@ async def test_private_client_cannot_write_to_shared(
         finally:
             await raw_memory_manager.delete_raw_memory(shared_memory.id, shared_writer_client)
 
-    async def test_private_client_can_modify_own_scope(
-        self, raw_memory_manager, private_client, test_user
-    ):
+    async def test_private_client_can_modify_own_scope(self, raw_memory_manager, private_client, test_user):
         """Test that private client can create, update, and delete in its own scope."""
         # Create in private scope
         memory = await raw_memory_manager.create_raw_memory(
@@ -596,15 +578,11 @@ async def test_no_access_client_cannot_read_any_memory(
         try:
             # no_access_client has read_scopes=[], so it cannot read anything
             with pytest.raises(NoResultFound):
-                await raw_memory_manager.get_raw_memory_by_id(
-                    memory.id, actor=no_access_client
-                )
+                await raw_memory_manager.get_raw_memory_by_id(memory.id, actor=no_access_client)
         finally:
             await raw_memory_manager.delete_raw_memory(memory.id, shared_writer_client)
 
-    async def test_no_access_client_cannot_create_memory(
-        self, raw_memory_manager, no_access_client, test_user
-    ):
+    async def test_no_access_client_cannot_create_memory(self, raw_memory_manager, no_access_client, test_user):
         """Test that a client with no write_scope cannot create memories."""
         memory_data = RawMemoryItemCreate(
             context="Attempting to create from no-access client",
@@ -688,9 +666,7 @@ async def test_client_cannot_read_outside_read_scopes(
             # shared_writer_client only has read_scopes=["shared"]
             # It should NOT be able to read 'private' scope memory
             with pytest.raises(NoResultFound):
-                await raw_memory_manager.get_raw_memory_by_id(
-                    private_memory.id, actor=shared_writer_client
-                )
+                await raw_memory_manager.get_raw_memory_by_id(private_memory.id, actor=shared_writer_client)
         finally:
             await raw_memory_manager.delete_raw_memory(private_memory.id, private_client)
 
diff --git a/tests/test_orm_to_pydantic_safe.py b/tests/test_orm_to_pydantic_safe.py
new file mode 100644
index 000000000..95997cc17
--- /dev/null
+++ b/tests/test_orm_to_pydantic_safe.py
@@ -0,0 +1,343 @@
+"""
+Test ORM to_pydantic() conversions to ensure they don't trigger MissingGreenlet errors.
+
+This test ensures that:
+1. ORM models can be safely converted to Pydantic even when detached from session
+2. Relationship access doesn't trigger lazy loading outside async context
+3. Meta agent and memory manager flows work correctly
+"""
+
+import pytest
+from sqlalchemy import select
+
+from mirix.orm import Agent as AgentModel
+from mirix.orm.episodic_memory import EpisodicEvent
+from mirix.orm.knowledge_vault import KnowledgeVaultItem
+from mirix.orm.procedural_memory import ProceduralMemoryItem
+from mirix.orm.resource_memory import ResourceMemoryItem
+from mirix.orm.semantic_memory import SemanticMemoryItem
+from mirix.schemas.agent import AgentState as PydanticAgentState
+from mirix.schemas.embedding_config import EmbeddingConfig
+from mirix.schemas.episodic_memory import EpisodicEvent as PydanticEpisodicEvent
+from mirix.schemas.llm_config import LLMConfig
+
+
+@pytest.mark.asyncio
+async def test_agent_to_pydantic_with_session(server):
+    """Test Agent.to_pydantic() inside an async session."""
+    from mirix.server.server import db_context
+
+    # Get test client
+    actor = server.default_client
+
+    # Create an agent with tools
+    from mirix.schemas.agent import CreateAgent
+
+    agent_create = CreateAgent(
+        name="test_agent_conversion",
+        llm_config=LLMConfig.default_config("gpt-4"),
+        embedding_config=EmbeddingConfig.default_config("text-embedding-004"),
+        include_base_tools=True,
+    )
+
+    agent_state = await server.agent_manager.create_agent(
+        agent_create=agent_create,
+        actor=actor,
+    )
+
+    # Now fetch it back and convert inside session
+    async with db_context() as session:
+        agent = await AgentModel.read(
+            db_session=session,
+            identifier=agent_state.id,
+            actor=actor,
+        )
+
+        # This should work - we're inside the session
+        pydantic_agent = agent.to_pydantic()
+
+        assert isinstance(pydantic_agent, PydanticAgentState)
+        assert pydantic_agent.id == agent_state.id
+        assert pydantic_agent.name == "test_agent_conversion"
+        # tools should be present (loaded via selectin)
+        assert isinstance(pydantic_agent.tools, list)
+
+
+@pytest.mark.asyncio
+async def test_agent_to_pydantic_detached(server):
+    """Test Agent.to_pydantic() on a detached instance (session closed)."""
+    from mirix.server.server import db_context
+
+    actor = server.default_client
+
+    # Create an agent
+    from mirix.schemas.agent import CreateAgent
+
+    agent_create = CreateAgent(
+        name="test_agent_detached",
+        llm_config=LLMConfig.default_config("gpt-4"),
+        embedding_config=EmbeddingConfig.default_config("text-embedding-004"),
+        include_base_tools=False,  # No tools to simplify
+    )
+
+    agent_state = await server.agent_manager.create_agent(
+        agent_create=agent_create,
+        actor=actor,
+    )
+
+    # Fetch agent and close session
+    async with db_context() as session:
+        agent = await AgentModel.read(
+            db_session=session,
+            identifier=agent_state.id,
+            actor=actor,
+        )
+        # Session closes here
+
+    # Now agent is detached - to_pydantic() should still work
+    # It should use cached/loaded relationships or empty list
+    pydantic_agent = agent.to_pydantic()
+
+    assert isinstance(pydantic_agent, PydanticAgentState)
+    assert pydantic_agent.id == agent_state.id
+    assert pydantic_agent.name == "test_agent_detached"
+    # tools might be empty list (not loaded) or loaded collection
+    assert isinstance(pydantic_agent.tools, list)
+
+
+@pytest.mark.asyncio
+async def test_episodic_memory_to_pydantic(server):
+    """Test EpisodicEvent.to_pydantic() doesn't trigger relationship loading."""
+    from datetime import datetime
+
+    from mirix.server.server import db_context
+
+    actor = server.default_client
+    user = server.admin_user
+
+    # Create an episodic event
+    from mirix.schemas.episodic_memory import EpisodicEvent as EpisodicEventCreate
+
+    event_data = {
+        "event_type": "test_event",
+        "actor": "system",
+        "summary": "Test event for conversion",
+        "details": "Testing to_pydantic conversion safety",
+        "occurred_at": datetime.now(),
+        "user_id": user.id,
+        "organization_id": user.organization_id,
+    }
+
+    event = await server.episodic_memory_manager.create_episodic_memory(
+        episodic_memory=EpisodicEventCreate(**event_data),
+        actor=actor,
+    )
+
+    # Fetch and convert inside session
+    async with db_context() as session:
+        result = await session.execute(select(EpisodicEvent).where(EpisodicEvent.id == event.id))
+        orm_event = result.scalar_one()
+
+        # Convert inside session
+        pydantic_event = orm_event.to_pydantic()
+        assert isinstance(pydantic_event, PydanticEpisodicEvent)
+        assert pydantic_event.id == event.id
+        assert pydantic_event.summary == "Test event for conversion"
+
+    # Now test after session closed
+    async with db_context() as session:
+        result = await session.execute(select(EpisodicEvent).where(EpisodicEvent.id == event.id))
+        orm_event = result.scalar_one()
+
+    # Session closed - to_pydantic() should still work
+    pydantic_event = orm_event.to_pydantic()
+    assert isinstance(pydantic_event, PydanticEpisodicEvent)
+    assert pydantic_event.id == event.id
+
+
+@pytest.mark.asyncio
+async def test_memory_models_to_pydantic(server):
+    """Test all memory models' to_pydantic() methods work safely."""
+    from mirix.server.server import db_context
+
+    actor = server.default_client
+    user = server.admin_user
+
+    # Test semantic memory
+    from mirix.schemas.semantic_memory import SemanticMemoryItem as SemanticCreate
+
+    semantic = await server.semantic_memory_manager.create_item(
+        item_data=SemanticCreate(
+            name="test_concept",
+            summary="Test summary",
+            details="Test details",
+            source="test",
+            user_id=user.id,
+            organization_id=user.organization_id,
+        ),
+        actor=actor,
+        user_id=user.id,
+    )
+
+    async with db_context() as session:
+        result = await session.execute(select(SemanticMemoryItem).where(SemanticMemoryItem.id == semantic.id))
+        orm_semantic = result.scalar_one()
+
+    # Detached conversion
+    pydantic_semantic = orm_semantic.to_pydantic()
+    assert pydantic_semantic.id == semantic.id
+    assert pydantic_semantic.name == "test_concept"
+
+    # Test procedural memory
+    from mirix.schemas.procedural_memory import ProceduralMemoryItem as ProceduralCreate
+
+    procedural = await server.procedural_memory_manager.create_item(
+        item_data=ProceduralCreate(
+            entry_type="workflow",
+            summary="test_procedure",
+            steps=["Step 1", "Step 2"],
+            user_id=user.id,
+            organization_id=user.organization_id,
+        ),
+        actor=actor,
+        user_id=user.id,
+    )
+
+    async with db_context() as session:
+        result = await session.execute(select(ProceduralMemoryItem).where(ProceduralMemoryItem.id == procedural.id))
+        orm_procedural = result.scalar_one()
+
+    pydantic_procedural = orm_procedural.to_pydantic()
+    assert pydantic_procedural.id == procedural.id
+    assert pydantic_procedural.summary == "test_procedure"
+
+    # Test resource memory
+    from mirix.schemas.resource_memory import ResourceMemoryItem as ResourceCreate
+
+    resource = await server.resource_memory_manager.create_item(
+        item_data=ResourceCreate(
+            title="test_resource_title",
+            summary="test_resource",
+            content="Resource content",
+            resource_type="document",
+            user_id=user.id,
+            organization_id=user.organization_id,
+        ),
+        actor=actor,
+        user_id=user.id,
+    )
+
+    async with db_context() as session:
+        result = await session.execute(select(ResourceMemoryItem).where(ResourceMemoryItem.id == resource.id))
+        orm_resource = result.scalar_one()
+
+    pydantic_resource = orm_resource.to_pydantic()
+    assert pydantic_resource.id == resource.id
+    assert pydantic_resource.summary == "test_resource"
+
+    # Test knowledge vault
+    from mirix.schemas.knowledge_vault import KnowledgeVaultItem as KnowledgeCreate
+
+    knowledge = await server.knowledge_vault_manager.create_item(
+        knowledge_vault_item=KnowledgeCreate(
+            entry_type="credential",
+            source="test",
+            sensitivity="low",
+            caption="test_knowledge",
+            secret_value="Secret data",
+            user_id=user.id,
+            organization_id=user.organization_id,
+        ),
+        actor=actor,
+        user_id=user.id,
+    )
+
+    async with db_context() as session:
+        result = await session.execute(select(KnowledgeVaultItem).where(KnowledgeVaultItem.id == knowledge.id))
+        orm_knowledge = result.scalar_one()
+
+    pydantic_knowledge = orm_knowledge.to_pydantic()
+    assert pydantic_knowledge.id == knowledge.id
+    assert pydantic_knowledge.caption == "test_knowledge"
+
+
+@pytest.mark.asyncio
+async def test_list_agents_conversion_safety(server):
+    """Test list_agents flow (simulating meta agent initialization)."""
+    actor = server.default_client
+
+    # Create multiple agents
+    from mirix.schemas.agent import CreateAgent
+
+    agent_names = ["meta_agent", "episodic_agent", "semantic_agent"]
+
+    for name in agent_names:
+        await server.agent_manager.create_agent(
+            agent_create=CreateAgent(
+                name=name,
+                llm_config=LLMConfig.default_config("gpt-4"),
+                embedding_config=EmbeddingConfig.default_config("text-embedding-004"),
+                include_base_tools=True,
+            ),
+            actor=actor,
+        )
+
+    # List agents (this is what MetaAgent does)
+    agents = await server.agent_manager.list_agents(actor=actor)
+
+    # Should have all our test agents
+    assert len(agents) >= 3
+
+    # All should be Pydantic models
+    for agent in agents:
+        assert isinstance(agent, PydanticAgentState)
+        assert agent.id is not None
+        assert isinstance(agent.tools, list)
+
+
+@pytest.mark.asyncio
+async def test_memory_manager_list_conversion(server):
+    """Test memory manager list_* methods convert safely."""
+    from datetime import datetime
+
+    actor = server.default_client
+    user = server.admin_user
+
+    # Create test data
+    from mirix.schemas.agent import CreateAgent
+
+    agent = await server.agent_manager.create_agent(
+        agent_create=CreateAgent(
+            name="test_memory_agent",
+            llm_config=LLMConfig.default_config("gpt-4"),
+            embedding_config=EmbeddingConfig.default_config("text-embedding-004"),
+        ),
+        actor=actor,
+    )
+
+    from mirix.schemas.episodic_memory import EpisodicEvent as EpisodicCreate
+
+    await server.episodic_memory_manager.create_episodic_memory(
+        episodic_memory=EpisodicCreate(
+            event_type="test",
+            actor="system",
+            summary="Test event",
+            details="Test details",
+            occurred_at=datetime.now(),
+            user_id=user.id,
+            organization_id=user.organization_id,
+        ),
+        actor=actor,
+    )
+
+    # List episodic memory (this is what memory tools do)
+    events = await server.episodic_memory_manager.list_episodic_memory(
+        agent_state=agent,
+        user=user,
+        query="",
+        limit=10,
+    )
+
+    # Should have at least our test event
+    assert len(events) >= 1
+    assert all(isinstance(e, PydanticEpisodicEvent) for e in events)
diff --git a/tests/test_queue.py b/tests/test_queue.py
index f2f4413ec..acf517755 100644
--- a/tests/test_queue.py
+++ b/tests/test_queue.py
@@ -43,18 +43,11 @@
 # ============================================================================
 
 
-@pytest_asyncio.fixture
-def event_loop():
-    """Single event loop for the module so DB managers and tests share one loop."""
-    loop = asyncio.new_event_loop()
-    yield loop
-    loop.close()
-
-
 @pytest_asyncio.fixture(scope="module", autouse=True)
 async def _init_db():
     """Create all DB tables before any test in this module touches the database."""
     from mirix.server.server import ensure_tables_created
+
     await ensure_tables_created()
 
 
@@ -65,9 +58,7 @@ async def ensure_organization():
     try:
         await org_mgr.get_organization_by_id(TEST_QUEUE_ORG_ID)
     except Exception:
-        await org_mgr.create_organization(
-            PydanticOrganization(id=TEST_QUEUE_ORG_ID, name="Test Queue Org")
-        )
+        await org_mgr.create_organization(PydanticOrganization(id=TEST_QUEUE_ORG_ID, name="Test Queue Org"))
     return TEST_QUEUE_ORG_ID
 
 
@@ -634,9 +625,7 @@ async def test_multiple_workers_partition_isolation(self, sample_client):
 
         def make_server(worker_key):
             s = Mock()
-            s.send_messages = AsyncMock(
-                side_effect=lambda **kwargs: processed[worker_key].append(kwargs["agent_id"])
-            )
+            s.send_messages = AsyncMock(side_effect=lambda **kwargs: processed[worker_key].append(kwargs["agent_id"]))
             s.client_manager = Mock()
             s.client_manager.get_client_by_id = AsyncMock(return_value=sample_client)
             return s
@@ -918,9 +907,7 @@ async def test_multiple_messages_processing(self, clean_manager, mock_server, sa
         await manager.cleanup()
 
     @pytest.mark.asyncio
-    async def test_worker_handles_processing_errors(
-        self, clean_manager, mock_server, sample_client, sample_messages
-    ):
+    async def test_worker_handles_processing_errors(self, clean_manager, mock_server, sample_client, sample_messages):
         manager = clean_manager
 
         mock_server.send_messages = AsyncMock(side_effect=Exception("Processing error"))
diff --git a/tests/test_raw_memory.py b/tests/test_raw_memory.py
index b07abded3..dfc94264e 100644
--- a/tests/test_raw_memory.py
+++ b/tests/test_raw_memory.py
@@ -41,8 +41,6 @@
 # =================================================================
 
 
-
-
 @pytest.fixture
 def raw_memory_manager():
     """Provide a RawMemoryManager instance."""
@@ -404,12 +402,8 @@ async def test_cleanup_job_deletes_stale_memories(raw_memory_manager, test_actor
 
         from mirix.orm.raw_memory import RawMemory
 
-        naive_utc_15_days_ago = (datetime.now(UTC).replace(tzinfo=None) - timedelta(days=15))
-        stmt = (
-            update(RawMemory)
-            .where(RawMemory.id == old_memory.id)
-            .values(updated_at=naive_utc_15_days_ago)
-        )
+        naive_utc_15_days_ago = datetime.now(UTC).replace(tzinfo=None) - timedelta(days=15)
+        stmt = update(RawMemory).where(RawMemory.id == old_memory.id).values(updated_at=naive_utc_15_days_ago)
         await session.execute(stmt)
         await session.commit()
 
@@ -465,10 +459,8 @@ async def test_cleanup_job_respects_custom_threshold(raw_memory_manager, test_ac
 
         from mirix.orm.raw_memory import RawMemory
 
-        naive_utc_8_days_ago = (datetime.now(UTC).replace(tzinfo=None) - timedelta(days=8))
-        stmt = (
-            update(RawMemory).where(RawMemory.id == memory.id).values(updated_at=naive_utc_8_days_ago)
-        )
+        naive_utc_8_days_ago = datetime.now(UTC).replace(tzinfo=None) - timedelta(days=8)
+        stmt = update(RawMemory).where(RawMemory.id == memory.id).values(updated_at=naive_utc_8_days_ago)
         await session.execute(stmt)
         await session.commit()
 
@@ -519,7 +511,7 @@ async def test_raw_memory_create_with_redis(raw_memory_manager, test_actor, test
     await raw_memory_manager.delete_raw_memory(created.id, test_actor)
 
 
-async def test_raw_memory_cache_hit_performance(raw_memory_manager, test_actor, test_user):
+async def test_raw_memory_cache_hit_performance(raw_memory_manager, test_actor, test_user, redis_client):
     """Test cache hit performance for raw memory reads."""
     memory_data = RawMemoryItemCreate(
         context="Redis test: Performance testing context",
@@ -818,13 +810,17 @@ async def test_api_create_and_get_raw_memory(api_client, raw_memory_manager, tes
 
 
 @pytest.mark.integration
-async def test_api_update_raw_memory_replace(api_client, raw_memory_manager, test_actor, test_user, mock_embedding_model):
+async def test_api_update_raw_memory_replace(
+    api_client, raw_memory_manager, test_actor, test_user, test_agent, mock_embedding_model
+):
     """Test PATCH /memory/raw/{memory_id} endpoint with replace mode."""
     import os
 
     api_key = os.getenv("GEMINI_API_KEY") or os.getenv("GOOGLE_API_KEY") or os.getenv("MIRIX_GOOGLE_API_KEY")
     if not api_key:
-        pytest.skip("Skipping API test with embeddings - no Google/Gemini API key (set GEMINI_API_KEY, GOOGLE_API_KEY, or MIRIX_GOOGLE_API_KEY)")
+        pytest.skip(
+            "Skipping API test with embeddings - no Google/Gemini API key (set GEMINI_API_KEY, GOOGLE_API_KEY, or MIRIX_GOOGLE_API_KEY)"
+        )
 
     # Create a raw memory first
     sample_data = RawMemoryItemCreate(
@@ -872,14 +868,16 @@ async def test_api_update_raw_memory_replace(api_client, raw_memory_manager, tes
 
 @pytest.mark.integration
 async def test_api_update_raw_memory_append_and_merge(
-    api_client, raw_memory_manager, test_actor, test_user, mock_embedding_model
+    api_client, raw_memory_manager, test_actor, test_user, test_agent, mock_embedding_model
 ):
     """Test PATCH /memory/raw/{memory_id} endpoint with append and merge modes."""
     import os
 
     api_key = os.getenv("GEMINI_API_KEY") or os.getenv("GOOGLE_API_KEY") or os.getenv("MIRIX_GOOGLE_API_KEY")
     if not api_key:
-        pytest.skip("Skipping API test with embeddings - no Google/Gemini API key (set GEMINI_API_KEY, GOOGLE_API_KEY, or MIRIX_GOOGLE_API_KEY)")
+        pytest.skip(
+            "Skipping API test with embeddings - no Google/Gemini API key (set GEMINI_API_KEY, GOOGLE_API_KEY, or MIRIX_GOOGLE_API_KEY)"
+        )
 
     # Create a raw memory first
     sample_data = RawMemoryItemCreate(
@@ -929,7 +927,7 @@ async def test_api_update_raw_memory_append_and_merge(
 
 
 @pytest.mark.integration
-async def test_api_delete_raw_memory(api_client, test_actor, test_user):
+async def test_api_delete_raw_memory(api_client, test_actor, test_user, test_agent):
     """Test DELETE /memory/raw/{memory_id} endpoint.
 
     Create via POST so create/delete/get all go through the same server (same DB and cache).
@@ -960,9 +958,9 @@ async def test_api_delete_raw_memory(api_client, test_actor, test_user):
 
     # GET after DELETE must return 404 (same server DB and cache)
     get_response = api_client.get(f"/memory/raw/{memory_id}", params={"user_id": test_user.id})
-    assert get_response.status_code == 404, (
-        f"GET after DELETE should return 404, got {get_response.status_code}: {get_response.text}"
-    )
+    assert (
+        get_response.status_code == 404
+    ), f"GET after DELETE should return 404, got {get_response.status_code}: {get_response.text}"
 
     print(f"\n[OK] DELETE /memory/raw/{memory_id} successful")
 
@@ -1870,7 +1868,7 @@ async def test_search_raw_memories_limit_enforcement(raw_memory_manager, test_ac
             user_id=test_user.id,
             use_cache=False,
         )
-        memories.append(mem    )
+        memories.append(mem)
 
     # Test limit=2
     results, _ = await raw_memory_manager.search_raw_memories(
diff --git a/tests/test_raw_memory_with_real_embeddings.py b/tests/test_raw_memory_with_real_embeddings.py
index dc77ac84d..d3faf3c55 100644
--- a/tests/test_raw_memory_with_real_embeddings.py
+++ b/tests/test_raw_memory_with_real_embeddings.py
@@ -84,7 +84,9 @@ async def main():
             raise ValueError("not found")
         print(f"[OK] Using existing organization: {org_id}")
     except Exception:
-        org = await org_mgr.create_organization(PydanticOrganization(id=org_id, name="Test Organization for Embeddings"))
+        org = await org_mgr.create_organization(
+            PydanticOrganization(id=org_id, name="Test Organization for Embeddings")
+        )
         print(f"[OK] Created organization: {org_id}")
 
     # Create client
diff --git a/tests/test_redis_integration.py b/tests/test_redis_integration.py
index 4e81fe450..a9215168f 100644
--- a/tests/test_redis_integration.py
+++ b/tests/test_redis_integration.py
@@ -38,15 +38,6 @@
 pytestmark = pytest.mark.asyncio(loop_scope="module")
 
 from mirix.database.redis_client import RedisMemoryClient, get_redis_client, initialize_redis_client
-
-
-@pytest.fixture(scope="module")
-def event_loop():
-    """Single event loop for the whole module so engine and Redis stay on one loop."""
-    loop = asyncio.new_event_loop()
-    yield loop
-    loop.close()
-
 from mirix.log import get_logger
 from mirix.schemas.agent import AgentType, CreateAgent, UpdateAgent
 from mirix.schemas.block import Block as PydanticBlock
@@ -91,39 +82,16 @@ def generate_test_id(prefix: str) -> str:
 
 
 @pytest_asyncio.fixture(scope="module", autouse=True)
-async def _ensure_server_and_redis_in_loop():
-    """Import server in the module event loop and use NullPool to avoid connection reuse issues."""
-    import mirix.server.server as server_module  # noqa: F401
-
-    # Use NullPool so each session gets a fresh connection (avoids 'another operation is in progress')
-    if (
-        hasattr(server_module, "engine")
-        and server_module.engine is not None
-        and "asyncpg" in str(server_module.engine.url)
-    ):
-        from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
-        from sqlalchemy.pool import NullPool
-
-        await server_module.engine.dispose()
-        _pg_uri = settings.mirix_pg_uri.replace("postgresql+pg8000://", "postgresql+asyncpg://").replace(
-            "postgresql://", "postgresql+asyncpg://"
-        )
-        server_module.engine = create_async_engine(_pg_uri, poolclass=NullPool, echo=settings.pg_echo)
-        server_module.AsyncSessionLocal = async_sessionmaker(
-            bind=server_module.engine,
-            class_=AsyncSession,
-            autocommit=False,
-            autoflush=False,
-            expire_on_commit=False,
-        )
+async def _ensure_tables_and_redis():
+    """Ensure DB tables exist (engine reset handled by conftest._reset_engine_per_module)."""
+    import mirix.server.server as server_module
 
     await server_module.ensure_tables_created()
-
     yield
 
 
 @pytest_asyncio.fixture
-async def redis_client(_ensure_server_and_redis_in_loop):
+async def redis_client(_ensure_tables_and_redis):
     """Redis client for tests: use a fresh client in this loop to avoid 'Future attached to different loop'."""
     if not settings.redis_enabled:
         pytest.skip("Redis not enabled - set MIRIX_REDIS_ENABLED=true")
@@ -213,61 +181,61 @@ async def test_client(test_organization):
 
 
 @pytest_asyncio.fixture
-async def block_manager(_ensure_server_and_redis_in_loop):
+async def block_manager(_ensure_tables_and_redis):
     """Create block manager instance (after server in loop)."""
     return BlockManager()
 
 
 @pytest_asyncio.fixture
-async def message_manager(_ensure_server_and_redis_in_loop):
+async def message_manager(_ensure_tables_and_redis):
     """Create message manager instance (after server in loop)."""
     return MessageManager()
 
 
 @pytest_asyncio.fixture
-async def episodic_manager(_ensure_server_and_redis_in_loop):
+async def episodic_manager(_ensure_tables_and_redis):
     """Create episodic memory manager instance (after server in loop)."""
     return EpisodicMemoryManager()
 
 
 @pytest_asyncio.fixture
-async def semantic_manager(_ensure_server_and_redis_in_loop):
+async def semantic_manager(_ensure_tables_and_redis):
     """Create semantic memory manager instance (after server in loop)."""
     return SemanticMemoryManager()
 
 
 @pytest_asyncio.fixture
-async def procedural_manager(_ensure_server_and_redis_in_loop):
+async def procedural_manager(_ensure_tables_and_redis):
     """Create procedural memory manager instance (after server in loop)."""
     return ProceduralMemoryManager()
 
 
 @pytest_asyncio.fixture
-async def resource_manager(_ensure_server_and_redis_in_loop):
+async def resource_manager(_ensure_tables_and_redis):
     """Create resource memory manager instance (after server in loop)."""
     return ResourceMemoryManager()
 
 
 @pytest_asyncio.fixture
-async def knowledge_manager(_ensure_server_and_redis_in_loop):
+async def knowledge_manager(_ensure_tables_and_redis):
     """Create knowledge vault manager instance (after server in loop)."""
     return KnowledgeVaultManager()
 
 
 @pytest_asyncio.fixture
-async def organization_manager(_ensure_server_and_redis_in_loop):
+async def organization_manager(_ensure_tables_and_redis):
     """Create organization manager (after server is imported in loop)."""
     return OrganizationManager()
 
 
 @pytest_asyncio.fixture
-async def user_manager(_ensure_server_and_redis_in_loop):
+async def user_manager(_ensure_tables_and_redis):
     """Create user manager instance (after server in loop)."""
     return UserManager()
 
 
 @pytest_asyncio.fixture(scope="module")
-async def ensure_admin_user(_ensure_server_and_redis_in_loop):
+async def ensure_admin_user(_ensure_tables_and_redis):
     """Ensure the admin user exists in the database.
 
     This is needed because agent creation creates messages that default
@@ -899,7 +867,9 @@ async def test_message_create_with_redis(self, message_manager, test_client, tes
         # Cleanup
         await message_manager.delete_message_by_id(created_message.id, test_client)
 
-    async def test_message_cache_hit_performance(self, message_manager, test_client, test_user, test_agent, redis_client):
+    async def test_message_cache_hit_performance(
+        self, message_manager, test_client, test_user, test_agent, redis_client
+    ):
         """Test message cache hit is significantly faster than DB."""
         # Create message
         message_data = PydanticMessage(
@@ -966,7 +936,9 @@ async def test_episodic_create_with_redis(self, episodic_manager, test_client, t
         # Cleanup
         await episodic_manager.delete_event_by_id(created_event.id, test_client)
 
-    async def test_episodic_cache_with_embeddings(self, episodic_manager, test_client, test_user, test_agent, redis_client):
+    async def test_episodic_cache_with_embeddings(
+        self, episodic_manager, test_client, test_user, test_agent, redis_client
+    ):
         """Test episodic memory with embeddings caches correctly."""
         # Create mock embeddings (4096 dimensions)
         mock_embedding = [0.1] * 4096
@@ -1108,7 +1080,9 @@ async def test_procedural_create_with_embeddings(
 class TestResourceMemoryManagerRedis:
     """Test Resource Memory Manager with Redis JSON caching (1 embedding)."""
 
-    async def test_resource_create_with_embedding(self, resource_manager, test_client, test_user, test_agent, redis_client):
+    async def test_resource_create_with_embedding(
+        self, resource_manager, test_client, test_user, test_agent, redis_client
+    ):
         """Test resource memory with 1 embedding (16KB) caches to Redis JSON."""
         # Create mock embedding
         from mirix.schemas.resource_memory import ResourceMemoryItem
@@ -1152,7 +1126,9 @@ async def test_resource_create_with_embedding(self, resource_manager, test_clien
 class TestKnowledgeVaultManagerRedis:
     """Test Knowledge Vault Manager with Redis JSON caching (1 embedding)."""
 
-    async def test_knowledge_create_with_embedding(self, knowledge_manager, test_client, test_user, test_agent, redis_client):
+    async def test_knowledge_create_with_embedding(
+        self, knowledge_manager, test_client, test_user, test_agent, redis_client
+    ):
         """Test knowledge vault item with 1 embedding (16KB) caches to Redis JSON."""
         # Create mock embedding
         from mirix.schemas.knowledge_vault import KnowledgeVaultItem
@@ -1263,7 +1239,9 @@ async def test_block_cache_speedup(self, block_manager, test_client, test_user,
         for block in blocks:
             await block_manager.delete_block(block.id, test_client)
 
-    async def test_message_cache_vs_db_comparison(self, message_manager, test_client, test_user, test_agent, redis_client):
+    async def test_message_cache_vs_db_comparison(
+        self, message_manager, test_client, test_user, test_agent, redis_client
+    ):
         """Compare Redis cache vs PostgreSQL performance for messages."""
         # Create test message
         message_data = PydanticMessage(
diff --git a/tests/test_scoped_blocks.py b/tests/test_scoped_blocks.py
index 4843a950e..2cad92717 100644
--- a/tests/test_scoped_blocks.py
+++ b/tests/test_scoped_blocks.py
@@ -31,42 +31,6 @@
 pytestmark = pytest.mark.asyncio(loop_scope="module")
 
 
-@pytest.fixture(scope="module")
-def event_loop():
-    """Single event loop for the module so shared fixtures and DB use one loop."""
-    loop = asyncio.new_event_loop()
-    yield loop
-    loop.close()
-
-
-@pytest_asyncio.fixture(scope="module", autouse=True)
-async def _ensure_server_in_loop():
-    """Import server in the module event loop and use NullPool to avoid connection reuse issues."""
-    import mirix.server.server as server_module  # noqa: F401
-
-    if (
-        hasattr(server_module, "engine")
-        and server_module.engine is not None
-        and "asyncpg" in str(server_module.engine.url)
-    ):
-        from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
-        from sqlalchemy.pool import NullPool
-
-        await server_module.engine.dispose()
-        _pg_uri = settings.mirix_pg_uri.replace("postgresql+pg8000://", "postgresql+asyncpg://").replace(
-            "postgresql://", "postgresql+asyncpg://"
-        )
-        server_module.engine = create_async_engine(_pg_uri, poolclass=NullPool, echo=settings.pg_echo)
-        server_module.AsyncSessionLocal = async_sessionmaker(
-            bind=server_module.engine,
-            class_=AsyncSession,
-            autocommit=False,
-            autoflush=False,
-            expire_on_commit=False,
-        )
-    yield
-
-
 # =============================================================================
 # Helpers
 # =============================================================================
@@ -82,7 +46,7 @@ def _test_id(prefix: str) -> str:
 
 
 @pytest_asyncio.fixture(scope="module")
-async def test_org(_ensure_server_in_loop):
+async def test_org():
     org_mgr = OrganizationManager()
     org_id = _test_id("scoped-blk-org")
     try:
@@ -988,7 +952,9 @@ async def test_two_clients_same_scope_share_blocks(self, block_manager, test_org
             )
         )
         blocks_via_a = await block_manager.get_blocks(user=target_user, any_scopes=[scope])
-        blocks_via_b = await block_manager.get_blocks(user=target_user, any_scopes=[scope], auto_create_from_default=False)
+        blocks_via_b = await block_manager.get_blocks(
+            user=target_user, any_scopes=[scope], auto_create_from_default=False
+        )
         assert {b.id for b in blocks_via_a} == {b.id for b in blocks_via_b}
 
     async def test_reader_client_sees_multiple_scopes(
@@ -1014,7 +980,9 @@ async def test_reader_client_sees_multiple_scopes(
         assert "test-scope-1" in scopes_found
         assert "test-scope-2" in scopes_found
 
-    async def test_reader_client_cannot_see_ungranted_scope(self, block_manager, client_scope1, client_scope2, test_org):
+    async def test_reader_client_cannot_see_ungranted_scope(
+        self, block_manager, client_scope1, client_scope2, test_org
+    ):
         """Reader with read_scopes=["test-scope-1"] cannot see test-scope-2 blocks."""
         restricted_reader = await ClientManager().create_client(
             PydanticClient(
diff --git a/tests/test_search_all_users.py b/tests/test_search_all_users.py
index ef74a7d74..0da28129d 100644
--- a/tests/test_search_all_users.py
+++ b/tests/test_search_all_users.py
@@ -18,7 +18,7 @@
 import os
 import time
 from pathlib import Path
-from typing import Optional
+from typing import Any, Awaitable, Callable, Optional
 
 import pytest
 import pytest_asyncio
@@ -28,6 +28,7 @@
 # Mark all tests as integration tests (require a running server)
 pytestmark = [
     pytest.mark.integration,
+    pytest.mark.usefixtures("isolate_api_key_env"),
 ]
 
 # Configure logging
@@ -41,6 +42,24 @@
 CONFIG_PATH = Path(__file__).parent.parent / "mirix" / "configs" / "examples" / "mirix_gemini.yaml"
 
 
+async def poll_until(
+    fetch_results: Callable[[], Awaitable[dict[str, Any]]],
+    is_ready: Callable[[dict[str, Any]], bool],
+    wait_log: str,
+    max_wait_s: int = 90,
+    interval_s: int = 15,
+) -> dict[str, Any]:
+    """Poll an async search until condition is met or timeout expires."""
+    results = await fetch_results()
+    elapsed = 0
+    while not is_ready(results) and elapsed < max_wait_s:
+        logger.info(wait_log, interval_s, elapsed)
+        await asyncio.sleep(interval_s)
+        elapsed += interval_s
+        results = await fetch_results()
+    return results
+
+
 async def add_all_memories(
     client: MirixClient,
     user_id: str,
@@ -197,13 +216,6 @@ class TestSearchAllUsers:
 
     pytestmark = [pytest.mark.asyncio(loop_scope="class")]
 
-    @pytest.fixture(scope="class")
-    def event_loop(self):
-        """Single event loop for the test class so all clients and tests share one loop."""
-        loop = asyncio.new_event_loop()
-        yield loop
-        loop.close()
-
     @pytest.fixture(scope="class")
     def client_scope_value(self):
         """Client scope value used for testing."""
@@ -374,11 +386,18 @@ async def test_search_all_users_with_client_id_retrieves_both_users(
         logger.info("TEST 3: Search with client_id retrieves both users with matching scope")
         logger.info("=" * 80)
 
-        results = await client1.search_all_users(
-            query="Python",  # Search for "Python" which should appear in semantic memories for both users
-            memory_type="all",
-            client_id=client1.client_id,
-            limit=50,
+        async def _search_client1_bm25():
+            return await client1.search_all_users(
+                query="Python",
+                memory_type="all",
+                client_id=client1.client_id,
+                limit=50,
+            )
+
+        results = await poll_until(
+            fetch_results=_search_client1_bm25,
+            is_ready=lambda r: r["count"] > 0,
+            wait_log=("Client1 bm25 search returned 0; waiting %ss before retry (elapsed=%ss)..."),
         )
 
         logger.info(f"Results: {results['count']} memories found")
@@ -421,12 +440,19 @@ async def test_search_all_users_with_client_id_retrieves_both_users_embedding(
         logger.info("TEST 3b: Embedding search with client_id retrieves both users with matching scope")
         logger.info("=" * 80)
 
-        results = await client1.search_all_users(
-            query="group discussion",  # Semantic query for "team meeting"
-            memory_type="all",
-            search_method="embedding",
-            client_id=client1.client_id,
-            limit=50,
+        async def _search_client1_embedding():
+            return await client1.search_all_users(
+                query="group discussion",
+                memory_type="all",
+                search_method="embedding",
+                client_id=client1.client_id,
+                limit=50,
+            )
+
+        results = await poll_until(
+            fetch_results=_search_client1_embedding,
+            is_ready=lambda r: r["count"] > 0,
+            wait_log=("Client1 embedding search returned 0; waiting %ss before retry (elapsed=%ss)..."),
         )
 
         logger.info(f"Results: {results['count']} memories found")
@@ -512,7 +538,14 @@ async def test_search_with_client3_retrieves_only_user3(self, client3, user3_id,
         logger.info("=" * 80)
 
         # Search with client3 which has write_scope='read_only'
-        results = await client3.search_all_users(query="", memory_type="all", client_id=client3.client_id, limit=100)
+        async def _search_client3_bm25():
+            return await client3.search_all_users(query="", memory_type="all", client_id=client3.client_id, limit=100)
+
+        results = await poll_until(
+            fetch_results=_search_client3_bm25,
+            is_ready=lambda r: user3_id in set(result["user_id"] for result in r["results"]),
+            wait_log=("Client3 bm25 search missing user3; waiting %ss before retry (elapsed=%ss)..."),
+        )
 
         logger.info(f"Results: {results['count']} memories found")
         logger.info(f"Filter Tags: {results.get('filter_tags')}")
@@ -535,12 +568,19 @@ async def test_search_with_client3_retrieves_only_user3_embedding(self, client3,
         logger.info("=" * 80)
 
         # Search with client3 which has write_scope='read_only'
-        results = await client3.search_all_users(
-            query="software development",  # Semantic query
-            memory_type="all",
-            search_method="embedding",
-            client_id=client3.client_id,
-            limit=100,
+        async def _search_client3_embedding():
+            return await client3.search_all_users(
+                query="software development",
+                memory_type="all",
+                search_method="embedding",
+                client_id=client3.client_id,
+                limit=100,
+            )
+
+        results = await poll_until(
+            fetch_results=_search_client3_embedding,
+            is_ready=lambda r: user3_id in set(result["user_id"] for result in r["results"]),
+            wait_log=("Client3 embedding search missing user3; waiting %ss before retry (elapsed=%ss)..."),
         )
 
         logger.info(f"Results: {results['count']} memories found")
@@ -566,8 +606,16 @@ async def test_search_different_org_no_cross_contamination(
         logger.info("TEST 8: Organization isolation - same scope, different org")
         logger.info("=" * 80)
 
-        # Search with client2 (in org2)
-        results = await client2.search_all_users(query="", memory_type="all", client_id=client2.client_id, limit=100)
+        # Search with client2 (in org2). Poll briefly because async memory
+        # extraction can lag under heavier CI/local runs.
+        async def _search_client2_bm25():
+            return await client2.search_all_users(query="", memory_type="all", client_id=client2.client_id, limit=100)
+
+        results = await poll_until(
+            fetch_results=_search_client2_bm25,
+            is_ready=lambda r: user4_id in set(result["user_id"] for result in r["results"]),
+            wait_log="Org2 search missing user4; waiting %ss before retry (elapsed=%ss)...",
+        )
 
         user_ids_in_results = set(result["user_id"] for result in results["results"])
         logger.info(f"Client 2 search - User IDs in results: {user_ids_in_results}")
@@ -590,12 +638,19 @@ async def test_search_different_org_no_cross_contamination_embedding(
         logger.info("=" * 80)
 
         # Search with client2 (in org2)
-        results = await client2.search_all_users(
-            query="database information",  # Semantic query
-            memory_type="all",
-            search_method="embedding",
-            client_id=client2.client_id,
-            limit=100,
+        async def _search_client2_embedding():
+            return await client2.search_all_users(
+                query="database information",
+                memory_type="all",
+                search_method="embedding",
+                client_id=client2.client_id,
+                limit=100,
+            )
+
+        results = await poll_until(
+            fetch_results=_search_client2_embedding,
+            is_ready=lambda r: user4_id in set(result["user_id"] for result in r["results"]),
+            wait_log=("Org2 embedding search missing user4; waiting %ss before retry (elapsed=%ss)..."),
         )
 
         user_ids_in_results = set(result["user_id"] for result in results["results"])
@@ -639,7 +694,9 @@ async def test_search_specific_memory_type(self, client1, user1_id, user2_id):
         logger.info("TEST: Search specific memory type (episodic)")
         logger.info("=" * 80)
 
-        results = await client1.search_all_users(query="team", memory_type="episodic", client_id=client1.client_id, limit=20)
+        results = await client1.search_all_users(
+            query="team", memory_type="episodic", client_id=client1.client_id, limit=20
+        )
 
         logger.info(f"Results: {results['count']} episodic memories found")
 
@@ -670,18 +727,8 @@ async def test_search_specific_memory_type_embedding(self, client1, user1_id, us
             limit=20,
         )
 
-        max_wait_s = 90
-        interval_s = 15
-        elapsed = 0
-        while results["count"] == 0 and elapsed < max_wait_s:
-            logger.info(
-                "Semantic embedding search returned 0; waiting %ss before retry (elapsed=%ds)...",
-                interval_s,
-                elapsed,
-            )
-            await asyncio.sleep(interval_s)
-            elapsed += interval_s
-            results = await client1.search_all_users(
+        async def _search_semantic_embedding():
+            return await client1.search_all_users(
                 query="programming language concepts",
                 memory_type="semantic",
                 search_method="embedding",
@@ -689,15 +736,20 @@ async def test_search_specific_memory_type_embedding(self, client1, user1_id, us
                 limit=20,
             )
 
+        results = await poll_until(
+            fetch_results=_search_semantic_embedding,
+            is_ready=lambda r: r["count"] > 0,
+            wait_log=("Semantic embedding search returned 0; waiting %ss before retry (elapsed=%ss)..."),
+        )
+
         logger.info(f"Results: {results['count']} semantic memories found")
         logger.info(f"Search Method: {results.get('search_method')}")
 
         assert results["success"] is True
         assert results["search_method"] == "embedding"
-        assert results["count"] > 0, (
-            "Semantic embedding search still 0 results after waiting %ds (index may not be ready)."
-            % max_wait_s
-        )
+        assert (
+            results["count"] > 0
+        ), "Semantic embedding search still 0 results after waiting for retries (index may not be ready)."
 
         # All results should be semantic type
         for result in results["results"]:
@@ -833,7 +885,9 @@ async def test_search_all_users_include_core_memory_returns_core_section(self, c
 
         assert results["success"] is True
         core_results = [r for r in results["results"] if r.get("memory_type") == "core"]
-        assert len(core_results) > 0, "Results should include items with memory_type='core' when include_core_memory=True"
+        assert (
+            len(core_results) > 0
+        ), "Results should include items with memory_type='core' when include_core_memory=True"
         for item in core_results:
             assert "id" in item
             assert "label" in item
@@ -873,9 +927,9 @@ async def test_search_all_users_include_core_memory_scope_isolation(self, client
             "Blocks from scope 'read_write' (client1's scope) must be returned. Scopes returned: %s" % scopes_returned
         )
         read_write_items = [r for r in core_results if r["scope"] == "read_write"]
-        assert len(read_write_items) > 0, (
-            "At least one block from scope 'read_write' must be returned. core count=%s" % len(core_results)
-        )
+        assert (
+            len(read_write_items) > 0
+        ), "At least one block from scope 'read_write' must be returned. core count=%s" % len(core_results)
 
         logger.info(
             "Scopes in core results: %s; read_write blocks: %s (read_only correctly excluded)",
diff --git a/tests/test_search_single_user_core_memory.py b/tests/test_search_single_user_core_memory.py
index 2ce0752dd..152f0bf37 100644
--- a/tests/test_search_single_user_core_memory.py
+++ b/tests/test_search_single_user_core_memory.py
@@ -26,6 +26,7 @@
 
 pytestmark = [
     pytest.mark.integration,
+    pytest.mark.usefixtures("isolate_api_key_env"),
 ]
 
 logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
@@ -203,12 +204,12 @@ async def test_core_memory_scope_isolation(self, client1, client2, user_id):
         scopes_a = set(r["scope"] for r in core_a)
         scopes_b = set(r["scope"] for r in core_b)
 
-        assert "scope_b" not in scopes_a, (
-            f"Client1 (scope_a) should not see scope_b blocks. Scopes returned: {scopes_a}"
-        )
-        assert "scope_a" not in scopes_b, (
-            f"Client2 (scope_b) should not see scope_a blocks. Scopes returned: {scopes_b}"
-        )
+        assert (
+            "scope_b" not in scopes_a
+        ), f"Client1 (scope_a) should not see scope_b blocks. Scopes returned: {scopes_a}"
+        assert (
+            "scope_a" not in scopes_b
+        ), f"Client2 (scope_b) should not see scope_a blocks. Scopes returned: {scopes_b}"
 
         if core_a:
             assert "scope_a" in scopes_a, f"Client1 should see scope_a blocks. Scopes: {scopes_a}"
@@ -238,9 +239,9 @@ async def test_include_core_memory_with_specific_memory_type(self, client1, user
         for r in non_core:
             assert r["memory_type"] == "episodic", "Non-core results should all be episodic"
 
-        assert len(core_results) > 0, (
-            "Core blocks should be returned even when memory_type='episodic' and include_core_memory=True"
-        )
+        assert (
+            len(core_results) > 0
+        ), "Core blocks should be returned even when memory_type='episodic' and include_core_memory=True"
         logger.info(
             "Test passed: %d core blocks + %d episodic results returned",
             len(core_results),
diff --git a/tests/test_temporal_queries.py b/tests/test_temporal_queries.py
index 5feebe208..664215b8b 100644
--- a/tests/test_temporal_queries.py
+++ b/tests/test_temporal_queries.py
@@ -163,9 +163,7 @@ def server_process():
             return
     except (requests.ConnectionError, requests.Timeout):
         pass
-    pytest.skip(
-        "Server not running. Start with: python scripts/start_server.py --port=8000"
-    )
+    pytest.skip("Server not running. Start with: python scripts/start_server.py --port=8000")
 
 
 @pytest_asyncio.fixture(scope="module")
@@ -173,9 +171,7 @@ async def api_auth(server_process):
     """Create org and client once per module; yield auth for client creation."""
     from conftest import _create_client_and_key
 
-    auth = await _create_client_and_key(
-        "temporal-test-client", "temporal-test-org", org_name="Temporal Test Org"
-    )
+    auth = await _create_client_and_key("temporal-test-client", "temporal-test-org", org_name="Temporal Test Org")
     os.environ.setdefault("MIRIX_API_URL", "http://localhost:8000")
     os.environ["MIRIX_API_KEY"] = auth["api_key"]
     return auth
@@ -235,9 +231,7 @@ async def test_retrieve_with_temporal_expression(self, temporal_client):
 
         result = await temporal_client.retrieve_with_conversation(
             user_id=TEST_USER_ID_TEMPORAL,
-            messages=[
-                {"role": "user", "content": [{"type": "text", "text": "What did I do today?"}]}
-            ],
+            messages=[{"role": "user", "content": [{"type": "text", "text": "What did I do today?"}]}],
             limit=10,
         )
 
@@ -262,9 +256,7 @@ async def test_retrieve_with_explicit_date_range(self, temporal_client):
 
         result = await temporal_client.retrieve_with_conversation(
             user_id=TEST_USER_ID_TEMPORAL,
-            messages=[
-                {"role": "user", "content": [{"type": "text", "text": "Show me November 2025 events"}]}
-            ],
+            messages=[{"role": "user", "content": [{"type": "text", "text": "Show me November 2025 events"}]}],
             limit=10,
             start_date=start,
             end_date=end,
@@ -293,9 +285,7 @@ async def test_temporal_filtering_episodic_only(self, temporal_client):
             messages=[
                 {
                     "role": "user",
-                    "content": [
-                        {"type": "text", "text": "I learned that Python uses list comprehensions."}
-                    ],
+                    "content": [{"type": "text", "text": "I learned that Python uses list comprehensions."}],
                 },
                 {"role": "assistant", "content": [{"type": "text", "text": "Noted."}]},
             ],
@@ -306,9 +296,7 @@ async def test_temporal_filtering_episodic_only(self, temporal_client):
         end = "2025-12-31T23:59:59"
         result = await temporal_client.retrieve_with_conversation(
             user_id=TEST_USER_ID_TEMPORAL,
-            messages=[
-                {"role": "user", "content": [{"type": "text", "text": "What do you know about me?"}]}
-            ],
+            messages=[{"role": "user", "content": [{"type": "text", "text": "What do you know about me?"}]}],
             limit=10,
             start_date=start,
             end_date=end,
diff --git a/tests/test_user.py b/tests/test_user.py
index 1156dd2a2..bedf3bafe 100644
--- a/tests/test_user.py
+++ b/tests/test_user.py
@@ -65,14 +65,6 @@ def server_check():
     )
 
 
-@pytest.fixture(scope="module")
-def event_loop():
-    """Single event loop for the module so client and tests share one loop."""
-    loop = asyncio.new_event_loop()
-    yield loop
-    loop.close()
-
-
 @pytest_asyncio.fixture
 async def client(server_check, api_auth):
     """Create a new MirixClient per test in the current loop (avoids closed-loop httpx)."""
@@ -118,7 +110,9 @@ async def test_explicit_user_creation_then_add_memory(client):
 
     # Step 2: Create user explicitly
     print(f"[Step 2] Creating user with create_or_get_user()...")
-    created_user_id = await client.create_or_get_user(user_id=user_id, user_name=f"Test User {user_id}", org_id=TEST_ORG_ID)
+    created_user_id = await client.create_or_get_user(
+        user_id=user_id, user_name=f"Test User {user_id}", org_id=TEST_ORG_ID
+    )
     print(f"[OK] User created: {created_user_id}")
     assert created_user_id == user_id, "Returned user_id should match requested user_id"
 
@@ -145,7 +139,9 @@ async def test_explicit_user_creation_then_add_memory(client):
 
     filter_tags = {"test_type": "explicit_creation", "account_id": "ACC-001"}
 
-    response = await client.add(user_id=user_id, messages=messages, filter_tags=filter_tags, chaining=False, verbose=False)
+    response = await client.add(
+        user_id=user_id, messages=messages, filter_tags=filter_tags, chaining=False, verbose=False
+    )
 
     print(f"[OK] Memory add request submitted")
     print(f"     Response: {response}")
@@ -212,7 +208,9 @@ async def test_auto_user_creation_on_add_memory(client):
 
     filter_tags = {"test_type": "auto_creation", "region": "West"}
 
-    response = await client.add(user_id=user_id, messages=messages, filter_tags=filter_tags, chaining=False, verbose=False)
+    response = await client.add(
+        user_id=user_id, messages=messages, filter_tags=filter_tags, chaining=False, verbose=False
+    )
 
     print(f"[OK] Memory add request submitted")
     print(f"     Response: {response}")
@@ -261,14 +259,18 @@ async def test_idempotent_create_or_get_user(client):
     user_id = f"test-idempotent-user-{uuid.uuid4().hex[:8]}"
     print(f"\n[Step 1] Creating user: {user_id}")
 
-    created_user_id_1 = await client.create_or_get_user(user_id=user_id, user_name="Idempotent Test User", org_id=TEST_ORG_ID)
+    created_user_id_1 = await client.create_or_get_user(
+        user_id=user_id, user_name="Idempotent Test User", org_id=TEST_ORG_ID
+    )
     print(f"[OK] User created (1st call): {created_user_id_1}")
 
     # Step 2: Call again with same user_id
     print(f"[Step 2] Calling create_or_get_user() again with same user_id...")
     await asyncio.sleep(1)  # Small delay
 
-    created_user_id_2 = await client.create_or_get_user(user_id=user_id, user_name="Idempotent Test User", org_id=TEST_ORG_ID)
+    created_user_id_2 = await client.create_or_get_user(
+        user_id=user_id, user_name="Idempotent Test User", org_id=TEST_ORG_ID
+    )
     print(f"[OK] User retrieved (2nd call): {created_user_id_2}")
 
     # Step 3: Verify same user_id returned
diff --git a/tests/test_user_manager.py b/tests/test_user_manager.py
index b1d9e8d03..be5327f06 100644
--- a/tests/test_user_manager.py
+++ b/tests/test_user_manager.py
@@ -64,46 +64,8 @@ def client_manager():
     return ClientManager()
 
 
-@pytest_asyncio.fixture(scope="module")
-def event_loop():
-    """Single event loop for the module so global DB engine stays on one loop."""
-    loop = asyncio.new_event_loop()
-    yield loop
-    loop.close()
-
-
-@pytest_asyncio.fixture(scope="module", autouse=True)
-async def _ensure_server_in_loop():
-    """Run server engine in the module event loop; use NullPool to avoid connection reuse."""
-    import mirix.server.server as server_module
-
-    if (
-        hasattr(server_module, "engine")
-        and server_module.engine is not None
-        and "asyncpg" in str(server_module.engine.url)
-    ):
-        from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker, create_async_engine
-        from sqlalchemy.pool import NullPool
-
-        await server_module.engine.dispose()
-        _pg_uri = settings.mirix_pg_uri.replace(
-            "postgresql+pg8000://", "postgresql+asyncpg://"
-        ).replace("postgresql://", "postgresql+asyncpg://")
-        server_module.engine = create_async_engine(
-            _pg_uri, poolclass=NullPool, echo=settings.pg_echo
-        )
-        server_module.AsyncSessionLocal = async_sessionmaker(
-            bind=server_module.engine,
-            class_=AsyncSession,
-            autocommit=False,
-            autoflush=False,
-            expire_on_commit=False,
-        )
-    yield
-
-
 @pytest_asyncio.fixture
-async def test_org1(_ensure_server_in_loop, organization_manager):
+async def test_org1(organization_manager):
     """Create test organization 1."""
     org = PydanticOrganization(id=generate_test_id("org"), name="Test Organization 1")
     created_org = await organization_manager.create_organization(org)
@@ -115,7 +77,7 @@ async def test_org1(_ensure_server_in_loop, organization_manager):
 
 
 @pytest_asyncio.fixture
-async def test_org2(_ensure_server_in_loop, organization_manager):
+async def test_org2(organization_manager):
     """Create test organization 2."""
     org = PydanticOrganization(id=generate_test_id("org"), name="Test Organization 2")
     created_org = await organization_manager.create_organization(org)
@@ -250,9 +212,7 @@ async def test_create_user_is_organization_scoped(self, user_manager, test_org1)
         except Exception:
             pass
 
-    async def test_same_user_id_retrieved_by_different_contexts(
-        self, user_manager, test_org1, client_a, client_b
-    ):
+    async def test_same_user_id_retrieved_by_different_contexts(self, user_manager, test_org1, client_a, client_b):
         """
         Verify that a user created in an org can be retrieved regardless of client context.
 
@@ -290,9 +250,7 @@ class TestMultipleClientsSameOrgShareUsers:
 
     pytestmark = pytest.mark.asyncio(loop_scope="module")
 
-    async def test_multiple_clients_same_org_see_same_users(
-        self, user_manager, test_org1, client_a, client_b
-    ):
+    async def test_multiple_clients_same_org_see_same_users(self, user_manager, test_org1, client_a, client_b):
         """
         Verify that two clients in the same organization see the same users.
 
@@ -330,9 +288,7 @@ async def test_multiple_clients_same_org_see_same_users(
                 except Exception:
                     pass
 
-    async def test_user_count_not_multiplied_by_clients(
-        self, user_manager, test_org1, client_a, client_b
-    ):
+    async def test_user_count_not_multiplied_by_clients(self, user_manager, test_org1, client_a, client_b):
         """
         Verify that having multiple clients doesn't multiply user count.
 
@@ -353,9 +309,7 @@ async def test_user_count_not_multiplied_by_clients(
             users = await user_manager.list_users(organization_id=test_org1.id)
             user_occurrences = [u for u in users if u.id == user_id]
 
-            assert len(user_occurrences) == 1, (
-                f"User should appear exactly once, got {len(user_occurrences)}"
-            )
+            assert len(user_occurrences) == 1, f"User should appear exactly once, got {len(user_occurrences)}"
 
         finally:
             try:
@@ -374,9 +328,7 @@ class TestUsersIsolatedAcrossOrganizations:
 
     pytestmark = pytest.mark.asyncio(loop_scope="module")
 
-    async def test_list_users_filters_by_organization(
-        self, user_manager, test_org1, test_org2
-    ):
+    async def test_list_users_filters_by_organization(self, user_manager, test_org1, test_org2):
         """
         Verify list_users filters by organization_id.
 
@@ -421,13 +373,9 @@ async def test_list_users_filters_by_organization(
             for uid in org2_user_ids:
                 assert uid in org2_retrieved_ids, f"Org2 user {uid} not in org2 list"
             for uid in org1_user_ids:
-                assert uid not in org2_retrieved_ids, (
-                    f"Org1 user {uid} should not be in org2 list"
-                )
+                assert uid not in org2_retrieved_ids, f"Org1 user {uid} should not be in org2 list"
             for uid in org2_user_ids:
-                assert uid not in org1_retrieved_ids, (
-                    f"Org2 user {uid} should not be in org1 list"
-                )
+                assert uid not in org1_retrieved_ids, f"Org2 user {uid} should not be in org1 list"
 
         finally:
             for uid in org1_user_ids + org2_user_ids:
@@ -447,9 +395,7 @@ class TestClientDeletionPreservesUsers:
 
     pytestmark = pytest.mark.asyncio(loop_scope="module")
 
-    async def test_delete_client_preserves_users(
-        self, user_manager, client_manager, test_org1
-    ):
+    async def test_delete_client_preserves_users(self, user_manager, client_manager, test_org1):
         """
         Verify deleting a client does NOT cascade-delete users.
 
@@ -483,9 +429,7 @@ async def test_delete_client_preserves_users(
             await client_manager.delete_client_by_id(client_id)
 
             user_after_delete = await user_manager.get_user_by_id(user_id)
-            assert user_after_delete.id == user_id, (
-                "User should still exist after client deletion"
-            )
+            assert user_after_delete.id == user_id, "User should still exist after client deletion"
             assert user_after_delete.organization_id == test_org1.id
 
         finally:
@@ -505,13 +449,9 @@ class TestGetOrCreateOrgDefaultUser:
 
     pytestmark = pytest.mark.asyncio(loop_scope="module")
 
-    async def test_get_or_create_org_default_user_creates_user(
-        self, user_manager, test_org1
-    ):
+    async def test_get_or_create_org_default_user_creates_user(self, user_manager, test_org1):
         """Verify get_or_create_org_default_user creates a default user for the org."""
-        default_user = await user_manager.get_or_create_org_default_user(
-            org_id=test_org1.id
-        )
+        default_user = await user_manager.get_or_create_org_default_user(org_id=test_org1.id)
 
         assert default_user is not None
         assert default_user.organization_id == test_org1.id
@@ -522,40 +462,24 @@ async def test_get_or_create_org_default_user_creates_user(
         except Exception:
             pass
 
-    async def test_get_or_create_org_default_user_is_idempotent(
-        self, user_manager, test_org1
-    ):
+    async def test_get_or_create_org_default_user_is_idempotent(self, user_manager, test_org1):
         """Verify get_or_create_org_default_user returns the same user on repeated calls."""
-        default_user_1 = await user_manager.get_or_create_org_default_user(
-            org_id=test_org1.id
-        )
-        default_user_2 = await user_manager.get_or_create_org_default_user(
-            org_id=test_org1.id
-        )
+        default_user_1 = await user_manager.get_or_create_org_default_user(org_id=test_org1.id)
+        default_user_2 = await user_manager.get_or_create_org_default_user(org_id=test_org1.id)
 
-        assert default_user_1.id == default_user_2.id, (
-            "Should return same user on repeated calls"
-        )
+        assert default_user_1.id == default_user_2.id, "Should return same user on repeated calls"
 
         try:
             await user_manager.delete_user_by_id(default_user_1.id)
         except Exception:
             pass
 
-    async def test_get_or_create_org_default_user_different_orgs(
-        self, user_manager, test_org1, test_org2
-    ):
+    async def test_get_or_create_org_default_user_different_orgs(self, user_manager, test_org1, test_org2):
         """Verify get_or_create_org_default_user creates separate users for different orgs."""
-        default_user_org1 = await user_manager.get_or_create_org_default_user(
-            org_id=test_org1.id
-        )
-        default_user_org2 = await user_manager.get_or_create_org_default_user(
-            org_id=test_org2.id
-        )
+        default_user_org1 = await user_manager.get_or_create_org_default_user(org_id=test_org1.id)
+        default_user_org2 = await user_manager.get_or_create_org_default_user(org_id=test_org2.id)
 
-        assert default_user_org1.id != default_user_org2.id, (
-            "Different orgs should have different default users"
-        )
+        assert default_user_org1.id != default_user_org2.id, "Different orgs should have different default users"
         assert default_user_org1.organization_id == test_org1.id
         assert default_user_org2.organization_id == test_org2.id