diff --git a/agents/templates/_partials/user-guidance-check.md b/agents/templates/_partials/user-guidance-check.md
index b9913b1..59aff5e 100644
--- a/agents/templates/_partials/user-guidance-check.md
+++ b/agents/templates/_partials/user-guidance-check.md
@@ -1 +1,3 @@
 **Check your context JSON for a `guidance` array.** If present, these are user-provided migration directives that you MUST follow. They take precedence over default heuristics.
+
+**If guidance explicitly allows a narrowly-scoped unsafe, ABI, or platform boundary when no safe equivalent exists, treat that as an allowed escape hatch.** Keep it minimal, audited, and isolated behind a safe API.
diff --git a/agents/templates/code-migrator.md b/agents/templates/code-migrator.md
index 2ffb7af..e3d854f 100644
--- a/agents/templates/code-migrator.md
+++ b/agents/templates/code-migrator.md
@@ -68,12 +68,24 @@ Concretely:
 
 The parity verifier will evaluate **behavioral equivalence** (same observable inputs → same observable outputs), not structural similarity. You will NOT be penalized for using different types, different function signatures, different module layouts, or different internal patterns — as long as the externally observable behavior is preserved.
 
+### Audited Unsafe Escape Hatch
+
+Default to safe, idiomatic target code. However, if a required source behavior cannot be reproduced faithfully with safe constructs alone, and the guidance explicitly permits it, you may use a narrowly-scoped unsafe or raw ABI/platform boundary.
+
+Rules:
+- Keep the unsafe or ABI boundary in a leaf helper or boundary module, not spread through the core algorithm logic.
+- Expose a safe wrapper to the rest of the codebase.
+- Do NOT use wrapper crates, bindgen, or delegation to the original implementation unless the guidance explicitly allows it.
+- Use unsafe only for parity-critical behavior, never for convenience or micro-optimization.
+- Add a brief inline comment documenting the invariant or boundary contract that makes the unsafe code sound.
+
 ### DO
 - Preserve all business logic and observable behavior exactly
 - Write idiomatic target-language code that a native developer would recognize
 - Use the target language's standard library, type system, and error model
 - Adapt API signatures to be natural in the target language
 - Handle edge cases identically to the source (same observable outcomes)
+- Use a narrowly-scoped audited unsafe or ABI boundary when parity requires it and the guidance explicitly allows it
 - Add inline comments noting migration decisions where behavior mapping is non-obvious
 
 ### DO NOT
@@ -83,6 +95,7 @@ The parity verifier will evaluate **behavioral equivalence** (same observable in
 - Attempt to migrate files outside your assigned task
 - Transliterate source-language idioms when a target-language idiom exists
 - Preserve source-language API shapes (pointer parameters, error codes, global state) when the target language has better patterns
+- Use unsafe or raw ABI calls for convenience, code brevity, or performance tuning
 - Read files beyond your task scope
 
 ## Handling Difficulties
diff --git a/agents/templates/parity-failure-resolver.md b/agents/templates/parity-failure-resolver.md
index cb3ab36..17d3c46 100644
--- a/agents/templates/parity-failure-resolver.md
+++ b/agents/templates/parity-failure-resolver.md
@@ -2,6 +2,8 @@
 
 {{> lore-index-first-principle}}
 
+{{> user-guidance-check}}
+
 You are the **Parity Failure Resolver** agent, invoked when a migration task cannot proceed cleanly (parity failure, build/test breakage, or blocked migration).
 
 {{> task-scope-awareness}}
@@ -23,6 +25,35 @@ Resolve the failing task quickly and safely by:
 
 When fixing parity issues, produce idiomatic target-language code — do NOT revert to source-language patterns to satisfy the verifier. If a parity issue stems from the verifier misidentifying an idiomatic target-language pattern as a gap (e.g., flagging `Result<T>` as not matching a C return code), set `scopeReduced: true` and explain in `notes` that the behavior is equivalent despite the structural difference. The goal is behavioral equivalence, not structural mimicry.
 
+When guidance explicitly allows a narrowly-scoped unsafe or platform boundary, treat that as an available recovery strategy. A small audited leaf shim is acceptable when it is the only way to preserve behavior and it does not delegate to the original source library.
+
+## Guidance-Constraint Adjudication
+
+Before attempting a code fix, check whether the reported parity issue **cannot be resolved without violating a `guidance` constraint**. This is the most common cause of oscillating parity failures across multiple attempts.
+
+If the guidance explicitly permits a narrowly-scoped unsafe or platform boundary, treat that as an available option rather than a prohibited one.
+
+**When to set `scopeReduced: true` instead of attempting a fix:**
+1. The source behavior depends on a language-specific runtime feature (e.g., compiler sanitizer hooks, inline assembly, FFI declarations) AND the guidance still prohibits the narrow unsafe/ABI/platform boundary needed to express it
+2. The `priorAttempts` array shows the same issue (or semantically equivalent issue) persisting across 2+ prior attempts despite different fix strategies — this is strong evidence the issue is fundamentally unresolvable within the guidance constraints
+3. The only viable fix would require violating an explicit guidance directive or expanding beyond the minimal unsafe/ABI escape hatch the guidance allows
+
+When adjudicating an issue as guidance-constrained:
+- Set `scopeReduced: true`
+- In `notes`, cite the specific guidance constraint that prevents resolution, explain why no conforming implementation can satisfy the verifier, and describe what the current implementation does as the best available approximation
+- Do NOT modify the code — leave the existing best-effort implementation in place
+- Set `strategyApplied` to `"Guidance-constraint adjudication"`
+
+## Allocator and Ownership Adjudication
+
+Do not treat a different internal allocation strategy as a parity failure unless the source exposes that memory behavior to callers. A Rust port may replace allocator plumbing with idiomatic ownership as long as caller-visible semantics stay the same.
+
+When reviewing allocator-related parity issues:
+- Ask whether the source exposes user-provided allocators, free callbacks, caller-owned buffers, or explicit ownership transfer in the public API
+- If not, prefer preserving observable behavior and leaving the idiomatic ownership model intact
+- Do NOT spend retry budget recreating C-style internal allocation plumbing purely to satisfy a structural reading of the source
+- If the verifier is objecting to an internal ownership change with no caller-visible divergence, explain that in `notes` and avoid unnecessary code churn
+
 ## Required Process
 
 1. **Diagnose**
diff --git a/agents/templates/parity-verifier.md b/agents/templates/parity-verifier.md
index d598c34..834fa9a 100644
--- a/agents/templates/parity-verifier.md
+++ b/agents/templates/parity-verifier.md
@@ -4,6 +4,8 @@ You are the **Parity Verifier** — a read-only analysis agent that checks wheth
 
 {{> lore-index-first-principle}}
 
+{{> user-guidance-check}}
+
 {{> task-scope-awareness}}
 
 **When `taskScope` is present, calibrate your analysis to the task's intended scope.** For example:
@@ -26,12 +28,42 @@ Parity means **behavioral equivalence** — the migrated code must produce the s
 - Different data structures (e.g., Vec instead of a linked list, HashMap instead of a red-black tree)
 - Different module organization or file layout
 - Different error handling patterns (e.g., Result/Option instead of sentinel return values)
-- Different memory management (e.g., ownership instead of malloc/free)
+- Different internal memory management or allocator strategy (e.g., ownership instead of malloc/free), unless the public API exposes allocator selection, ownership transfer, or caller-managed memory semantics that have changed
 - Merged or split functions, renamed identifiers, or reorganized types — as long as all behavior is preserved
 - Use of target-language standard library where the source used hand-rolled implementations
 
 Do NOT flag idiomatic target-language patterns as parity issues. A Rust `Result<T, E>` is equivalent to a C `int` return code + out-parameter if it conveys the same success/failure semantics.
 
+## Guidance-Constrained Parity
+
+When the `guidance` array is present in your context, some source behaviors may be **intentionally impossible to replicate** in the target due to user-imposed constraints. Common examples include:
+- Source code that relies on language-specific runtime features (sanitizer hooks, compiler intrinsics, FFI declarations) when guidance prohibits unsafe code or FFI in the target
+- Platform-specific system calls when guidance requires a pure/portable implementation
+- Source patterns that depend on undefined behavior when guidance requires safe, well-defined code
+
+**When a source behavior cannot be faithfully reproduced without violating a guidance constraint:**
+- Classify the issue as `minor`, not `major` or `critical`
+- In the `details` field, explicitly note which guidance constraint makes faithful reproduction impossible
+- In the `suggestedFix` field, recommend the best available approximation that respects the guidance (e.g., no-op behind a feature flag, compile-time constant, or documented deviation)
+
+When guidance explicitly permits a narrowly-scoped unsafe or platform boundary as the only viable way to preserve behavior:
+- Evaluate whether the unsafe/ABI surface is minimal, audited, and isolated behind a safe API
+- Do NOT prefer a less faithful safe-only approximation over a minimal allowed boundary that preserves behavior
+
+Do NOT flag source behaviors as `major` or `critical` when the only path to resolution would require violating a user-provided guidance directive. The guidance constraints represent deliberate user decisions and take precedence over source-faithful reproduction.
+
+## Allocator and Ownership Contract Parity
+
+Changes to the target's internal allocation model do NOT by themselves create a parity failure. A Rust port may replace malloc/free plumbing, arena internals, or ad-hoc ownership tracking with RAII, Vec, Box, Arc, or other idiomatic constructs as long as callers observe the same behavior.
+
+Only flag allocator-related issues as `major` or `critical` when the source exposes memory behavior as part of the public contract, such as:
+- User-supplied allocators or custom free callbacks
+- Caller-owned buffers, explicit transfer-of-ownership rules, or required deallocation order
+- Public aliasing/lifetime guarantees that affect correctness
+- Allocation-failure behavior or size/accounting semantics that change observable results
+
+If the difference is purely internal representation or ownership discipline, do NOT describe it as a public-contract divergence.
+
 ## Responsibilities
 
 1. **Behavioral Parity**
@@ -76,6 +108,7 @@ Do NOT flag idiomatic target-language patterns as parity issues. A Rust `Result<
    - Check whether the target function implements the algorithm natively or delegates to an external binding/wrapper of the source library
    - If the target calls into a package that wraps or binds to the source library via FFI, flag as `critical` — the migration has not actually re-implemented the logic
    - If the target imports or links against the source library's compiled artifacts, flag as `critical`
+   - Do NOT flag a minimal OS/runtime ABI shim as delegation if it does not call the original source library and the migrated algorithm remains natively implemented in the target
    - Compare the target function's implementation depth against the source: a source function with substantial algorithm logic should not map to a short target function that delegates to a library call
 
 9. **Hollow Implementation Detection** (severity guidance: `critical`)
diff --git a/package-lock.json b/package-lock.json
index edbd064..3bf6e70 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -9,7 +9,7 @@
       "version": "0.1.0",
       "dependencies": {
         "@cadre-dev/framework": "^0.2.5",
-        "@jafreck/lore": "^0.3.9",
+        "@jafreck/lore": "0.4.0",
         "@modelcontextprotocol/sdk": "^1.27.1",
         "@types/better-sqlite3": "^7.6.13",
         "better-sqlite3": "^12.6.2",
@@ -1134,45 +1134,20 @@
       }
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-      "resolved": "https://registry.npmjs.org/@jafreck/lore/-/lore-0.3.9.tgz",
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+      "version": "0.4.0",
+      "resolved": "https://registry.npmjs.org/@jafreck/lore/-/lore-0.4.0.tgz",
+      "integrity": "sha512-yq4n514nnFwRf/pESOO7NNV8uZRxCx8dgLvUlVakUaiepcCy2Zcji7JjrUCPogqi+2WbOI9d8TQnZ5g/lQRt5g==",
       "license": "MIT",
       "dependencies": {
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-        "@elm-tooling/tree-sitter-elm": "^5.9.0",
         "@huggingface/transformers": "^3.8.1",
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         "@sourcegraph/scip-python": "^0.6.6",
         "@sourcegraph/scip-typescript": "^0.4.0",
-        "@tree-sitter-grammars/tree-sitter-lua": "^0.4.1",
-        "@tree-sitter-grammars/tree-sitter-zig": "^1.1.2",
         "better-sqlite3": "^12.6.2",
         "fast-glob": "^3.3.3",
-        "node-gyp-build": "^4.8.4",
         "simple-git": "^3.32.3",
         "sqlite-vec": "^0.1.6",
-        "tree-sitter": "0.25.0",
-        "tree-sitter-bash": "^0.25.1",
-        "tree-sitter-c": "^0.24.1",
-        "tree-sitter-c-sharp": "^0.23.1",
-        "tree-sitter-cpp": "^0.23.4",
-        "tree-sitter-elixir": "^0.3.5",
-        "tree-sitter-go": ">=0.23.4",
-        "tree-sitter-haskell": "^0.23.1",
-        "tree-sitter-java": "^0.23.5",
-        "tree-sitter-javascript": "^0.25.0",
-        "tree-sitter-julia": "^0.23.1",
-        "tree-sitter-kotlin": "^0.3.8",
-        "tree-sitter-objc": "^3.0.2",
-        "tree-sitter-ocaml": "^0.24.2",
-        "tree-sitter-php": "^0.24.2",
-        "tree-sitter-python": ">=0.23.6",
-        "tree-sitter-ruby": "^0.23.1",
-        "tree-sitter-rust": "^0.24.0",
-        "tree-sitter-scala": "^0.24.0",
-        "tree-sitter-swift": "^0.7.1",
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         "zod": "^4.3"
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       "bin": {
@@ -1182,349 +1157,6 @@
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-      },
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-        "node-gyp-build": "^4.8.0"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.21.0"
-      },
-      "peerDependenciesMeta": {
-        "tree_sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/@jafreck/lore/node_modules/tree-sitter-kotlin/node_modules/node-addon-api": {
-      "version": "7.1.1",
-      "resolved": "https://registry.npmjs.org/node-addon-api/-/node-addon-api-7.1.1.tgz",
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-      "license": "MIT"
-    },
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-        }
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-    "node_modules/@jafreck/lore/node_modules/tree-sitter-ruby": {
-      "version": "0.23.1",
-      "resolved": "https://registry.npmjs.org/tree-sitter-ruby/-/tree-sitter-ruby-0.23.1.tgz",
-      "integrity": "sha512-d9/RXgWjR6HanN7wTYhS5bpBQLz1VkH048Vm3CodPGyJVnamXMGb8oEhDypVCBq4QnHui9sTXuJBBP3WtCw5RA==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
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-        "node-gyp-build": "^4.8.2"
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-      "peerDependencies": {
-        "tree-sitter": "^0.21.1"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/@jafreck/lore/node_modules/tree-sitter-scala": {
-      "version": "0.24.0",
-      "resolved": "https://registry.npmjs.org/tree-sitter-scala/-/tree-sitter-scala-0.24.0.tgz",
-      "integrity": "sha512-vkMuAUrBZ1zZz2XcGDQk18Kz73JkpgaeXzbNVobPke0G35sd9jH32aUxG6OLRKM7et0TbsfqkWf4DeJoGk4K1g==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.2.2",
-        "node-gyp-build": "^4.8.2"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.21.1"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/@jafreck/lore/node_modules/tree-sitter-typescript": {
-      "version": "0.23.2",
-      "resolved": "https://registry.npmjs.org/tree-sitter-typescript/-/tree-sitter-typescript-0.23.2.tgz",
-      "integrity": "sha512-e04JUUKxTT53/x3Uq1zIL45DoYKVfHH4CZqwgZhPg5qYROl5nQjV+85ruFzFGZxu+QeFVbRTPDRnqL9UbU4VeA==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.2.2",
-        "node-gyp-build": "^4.8.2",
-        "tree-sitter-javascript": "^0.23.1"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.21.0"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/@jafreck/lore/node_modules/tree-sitter-typescript/node_modules/tree-sitter-javascript": {
-      "version": "0.23.1",
-      "resolved": "https://registry.npmjs.org/tree-sitter-javascript/-/tree-sitter-javascript-0.23.1.tgz",
-      "integrity": "sha512-/bnhbrTD9frUYHQTiYnPcxyHORIw157ERBa6dqzaKxvR/x3PC4Yzd+D1pZIMS6zNg2v3a8BZ0oK7jHqsQo9fWA==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.2.2",
-        "node-gyp-build": "^4.8.2"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.21.1"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
     "node_modules/@jridgewell/resolve-uri": {
       "version": "3.1.2",
       "resolved": "https://registry.npmjs.org/@jridgewell/resolve-uri/-/resolve-uri-3.1.2.tgz",
@@ -2066,44 +1698,6 @@
       "dev": true,
       "license": "MIT"
     },
-    "node_modules/@tree-sitter-grammars/tree-sitter-lua": {
-      "version": "0.4.1",
-      "resolved": "https://registry.npmjs.org/@tree-sitter-grammars/tree-sitter-lua/-/tree-sitter-lua-0.4.1.tgz",
-      "integrity": "sha512-EwagFaU6ZveVk18/Y8qUhZkkiBKnQ7dSCHbm//TUroLVKy3i1rOYGy/cNHtSkAb1eDvS1HhCLybH2S541Cya/g==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.5.0",
-        "node-gyp-build": "^4.8.4"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.4"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/@tree-sitter-grammars/tree-sitter-zig": {
-      "version": "1.1.2",
-      "resolved": "https://registry.npmjs.org/@tree-sitter-grammars/tree-sitter-zig/-/tree-sitter-zig-1.1.2.tgz",
-      "integrity": "sha512-J0L31HZ2isy3F5zb2g5QWQOv2r/pbruQNL9ADhuQv2pn5BQOzxt80WcEJaYXBeuJ8GHxVT42slpCna8k1c8LOw==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.3.0",
-        "node-gyp-build": "^4.8.4"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.1"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
     "node_modules/@tsconfig/node10": {
       "version": "1.0.12",
       "resolved": "https://registry.npmjs.org/@tsconfig/node10/-/node10-1.0.12.tgz",
@@ -4222,26 +3816,6 @@
         "node": ">=10"
       }
     },
-    "node_modules/node-addon-api": {
-      "version": "8.6.0",
-      "resolved": "https://registry.npmjs.org/node-addon-api/-/node-addon-api-8.6.0.tgz",
-      "integrity": "sha512-gBVjCaqDlRUk0EwoPNKzIr9KkS9041G/q31IBShPs1Xz6UTA+EXdZADbzqAJQrpDRq71CIMnOP5VMut3SL0z5Q==",
-      "license": "MIT",
-      "engines": {
-        "node": "^18 || ^20 || >= 21"
-      }
-    },
-    "node_modules/node-gyp-build": {
-      "version": "4.8.4",
-      "resolved": "https://registry.npmjs.org/node-gyp-build/-/node-gyp-build-4.8.4.tgz",
-      "integrity": "sha512-LA4ZjwlnUblHVgq0oBF3Jl/6h/Nvs5fzBLwdEF4nuxnFdsfajde4WfxtJr3CaiH+F6ewcIB/q4jQ4UzPyid+CQ==",
-      "license": "MIT",
-      "bin": {
-        "node-gyp-build": "bin.js",
-        "node-gyp-build-optional": "optional.js",
-        "node-gyp-build-test": "build-test.js"
-      }
-    },
     "node_modules/object-assign": {
       "version": "4.1.1",
       "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz",
@@ -5337,167 +4911,6 @@
         "node": ">=0.6"
       }
     },
-    "node_modules/tree-sitter": {
-      "version": "0.22.4",
-      "resolved": "https://registry.npmjs.org/tree-sitter/-/tree-sitter-0.22.4.tgz",
-      "integrity": "sha512-usbHZP9/oxNsUY65MQUsduGRqDHQOou1cagUSwjhoSYAmSahjQDAVsh9s+SlZkn8X8+O1FULRGwHu7AFP3kjzg==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "peer": true,
-      "dependencies": {
-        "node-addon-api": "^8.3.0",
-        "node-gyp-build": "^4.8.4"
-      }
-    },
-    "node_modules/tree-sitter-c": {
-      "version": "0.24.1",
-      "resolved": "https://registry.npmjs.org/tree-sitter-c/-/tree-sitter-c-0.24.1.tgz",
-      "integrity": "sha512-lkYwWN3SRecpvaeqmFKkuPNR3ZbtnvHU+4XAEEkJdrp3JfSp2pBrhXOtvfsENUneye76g889Y0ddF2DM0gEDpA==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.3.1",
-        "node-gyp-build": "^4.8.4"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.4"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/tree-sitter-cli": {
-      "version": "0.23.2",
-      "resolved": "https://registry.npmjs.org/tree-sitter-cli/-/tree-sitter-cli-0.23.2.tgz",
-      "integrity": "sha512-kPPXprOqREX+C/FgUp2Qpt9jd0vSwn+hOgjzVv/7hapdoWpa+VeWId53rf4oNNd29ikheF12BYtGD/W90feMbA==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "bin": {
-        "tree-sitter": "cli.js"
-      },
-      "engines": {
-        "node": ">=12.0.0"
-      }
-    },
-    "node_modules/tree-sitter-objc": {
-      "version": "3.0.2",
-      "resolved": "https://registry.npmjs.org/tree-sitter-objc/-/tree-sitter-objc-3.0.2.tgz",
-      "integrity": "sha512-Hs0ohmx1u5M+0K7efoW+dv/corhBsfjftfIYLtp7dSGeJ+Zj4c33tDIboBYLs6qijRlz6wtHFxa0YX+FibLulA==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.3.0",
-        "node-gyp-build": "^4.8.4",
-        "tree-sitter-c": "^0.23.4"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.1"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/tree-sitter-objc/node_modules/tree-sitter-c": {
-      "version": "0.23.6",
-      "resolved": "https://registry.npmjs.org/tree-sitter-c/-/tree-sitter-c-0.23.6.tgz",
-      "integrity": "sha512-0dxXKznVyUA0s6PjNolJNs2yF87O5aL538A/eR6njA5oqX3C3vH4vnx3QdOKwuUdpKEcFdHuiDpRKLLCA/tjvQ==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.3.0",
-        "node-gyp-build": "^4.8.4"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.1"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/tree-sitter-ocaml": {
-      "version": "0.24.2",
-      "resolved": "https://registry.npmjs.org/tree-sitter-ocaml/-/tree-sitter-ocaml-0.24.2.tgz",
-      "integrity": "sha512-H0RAeCepIyXyTPCQra6yMd7Bn5ZBYkIaddzdLNwVZpM9mCe2e8av+3O6Ojl7Z8YHrV/kYsfHvI2y+Hh7qzcYQQ==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.3.0",
-        "node-gyp-build": "^4.8.4"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.4"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/tree-sitter-php": {
-      "version": "0.24.2",
-      "resolved": "https://registry.npmjs.org/tree-sitter-php/-/tree-sitter-php-0.24.2.tgz",
-      "integrity": "sha512-zwgAePc/HozNaWOOfwRAA+3p8yhuehRw8Fb7vn5qd2XjiIc93uJPryDTMYTSjBRjVIUg/KY6pM3rRzs8dSwKfw==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.2.2",
-        "node-gyp-build": "^4.8.2"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.4"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/tree-sitter-rust": {
-      "version": "0.24.0",
-      "resolved": "https://registry.npmjs.org/tree-sitter-rust/-/tree-sitter-rust-0.24.0.tgz",
-      "integrity": "sha512-NWemUDf629Tfc90Y0Z55zuwPCAHkLxWnMf2RznYu4iBkkrQl2o/CHGB7Cr52TyN5F1DAx8FmUnDtCy9iUkXZEQ==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.2.2",
-        "node-gyp-build": "^4.8.4"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.1"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/tree-sitter-swift": {
-      "version": "0.7.1",
-      "resolved": "https://registry.npmjs.org/tree-sitter-swift/-/tree-sitter-swift-0.7.1.tgz",
-      "integrity": "sha512-pneKVTuGamaBsqqqfB9BvNQjktzh/0IVPR54jLB5Fq/JTDQwYHd0Wo6pVyZ5jAYpbztzq+rJ/rpL9ruxTmSoKw==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "dependencies": {
-        "node-addon-api": "^8.0.0",
-        "node-gyp-build": "^4.8.0",
-        "tree-sitter-cli": "^0.23",
-        "which": "2.0.2"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.22.1"
-      },
-      "peerDependenciesMeta": {
-        "tree_sitter": {
-          "optional": true
-        }
-      }
-    },
     "node_modules/ts-node": {
       "version": "10.9.2",
       "resolved": "https://registry.npmjs.org/ts-node/-/ts-node-10.9.2.tgz",
diff --git a/package.json b/package.json
index 0fc9ca2..1b4b65e 100644
--- a/package.json
+++ b/package.json
@@ -20,7 +20,7 @@
   },
   "dependencies": {
     "@cadre-dev/framework": "^0.2.5",
-    "@jafreck/lore": "^0.3.9",
+    "@jafreck/lore": "0.4.0",
     "@modelcontextprotocol/sdk": "^1.27.1",
     "@types/better-sqlite3": "^7.6.13",
     "better-sqlite3": "^12.6.2",
diff --git a/src/agents/agent-output-schemas.ts b/src/agents/agent-output-schemas.ts
index b2a97a5..d3ab0ce 100644
--- a/src/agents/agent-output-schemas.ts
+++ b/src/agents/agent-output-schemas.ts
@@ -27,6 +27,56 @@ export const AamfOutputBase = z.object({
 
 export type AamfOutputBaseType = z.infer<typeof AamfOutputBase>;
 
+function isRecord(value: unknown): value is Record<string, unknown> {
+  return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+
+function normalizeLegacyStatus(status: unknown): unknown {
+  if (typeof status !== 'string') return status;
+
+  switch (status.trim().toLowerCase()) {
+    case 'success':
+    case 'succeeded':
+    case 'ok':
+      return 'completed';
+    case 'needs_review':
+    case 'needs review':
+      return 'needs-review';
+    case 'error':
+    case 'failure':
+      return 'failed';
+    default:
+      return status;
+  }
+}
+
+function normalizeLegacyNotes(notes: unknown): unknown {
+  if (!Array.isArray(notes) || !notes.every(item => typeof item === 'string')) {
+    return notes;
+  }
+
+  return notes.join('\n');
+}
+
+function normalizeAamfOutput(raw: unknown): unknown {
+  if (!isRecord(raw)) return raw;
+
+  const normalized: Record<string, unknown> = { ...raw };
+
+  normalized.status = normalizeLegacyStatus(normalized.status);
+  normalized.notes = normalizeLegacyNotes(normalized.notes);
+
+  if (
+    normalized.outputFiles === undefined
+    && Array.isArray(normalized.written)
+    && normalized.written.every(item => typeof item === 'string')
+  ) {
+    normalized.outputFiles = normalized.written;
+  }
+
+  return normalized;
+}
+
 /**
  * JSON schema for structured agent task results.
  * @deprecated Parity results are now extracted from aamf-json output directly.
@@ -107,6 +157,8 @@ export function parseAamfOutput<T extends z.ZodTypeAny>(
     }
   }
 
+  raw = normalizeAamfOutput(raw);
+
   const result = schema.safeParse(raw);
   if (!result.success) {
     return { parsed: false, error: `schema validation failed: ${result.error.message}` };
diff --git a/src/config/schema.ts b/src/config/schema.ts
index f8d3165..3934799 100644
--- a/src/config/schema.ts
+++ b/src/config/schema.ts
@@ -11,7 +11,7 @@ export const MigrationConfigSchema = z.object({
    *
    * Examples:
    *   - "Do NOT use any existing crates/packages that wrap the C implementation."
-   *   - "Write a pure native Rust port — no FFI or bindgen."
+  *   - "Write a pure native Rust port — no wrapper crates or bindgen; allow only audited leaf unsafe/ABI shims when no safe equivalent exists."
    *   - "Preserve the original directory layout in the target output."
    */
   guidance: z.array(z.string().min(1)).optional(),
@@ -194,8 +194,10 @@ export const MigrationConfigSchema = z.object({
     }).optional(),
     /**
      * Options for KB indexing (Phase 0).
-     * The Lore indexer always runs in Phase 0 to build a SQLite knowledge-base.
-     * An HTTP MCP server is started for agents to query it.
+      * The Lore indexer always runs in Phase 0 to build a SQLite knowledge-base.
+      * SCIP indexing is always enabled; optional LSP enrichment augments the
+      * baseline index and powers overlay updates.
+      * An HTTP MCP server is started for agents to query it.
      */
     kbIndex: z.object({
       /**
@@ -223,14 +225,14 @@ export const MigrationConfigSchema = z.object({
         pythonBin: z.string().default('python3'),
       }).optional(),
       /**
-       * LSP integration for the Lore indexer.
+       * Optional LSP enrichment for the Lore indexer.
        * When enabled, Lore starts language servers (e.g. clangd for C/C++,
-       * typescript-language-server for TS) to resolve cross-file symbol
-       * references, type definitions, and call targets with full semantic
-       * accuracy — beyond what tree-sitter can provide alone.
+       * typescript-language-server for TS) to enrich symbols and refs with
+       * semantic definition and type information, and to power overlay updates
+       * after the baseline SCIP index is built.
        */
       lsp: z.object({
-        /** Enable LSP-powered symbol resolution during indexing. Default: false. */
+        /** Enable LSP enrichment and overlay updates. Default: false. */
         enabled: z.boolean().default(false),
         /** Timeout in ms for each LSP request (hover, definition, references). */
         requestTimeoutMs: z.number().int().min(500).default(5000),
diff --git a/src/core/checkpoint.ts b/src/core/checkpoint.ts
index 62c1286..46c3849 100644
--- a/src/core/checkpoint.ts
+++ b/src/core/checkpoint.ts
@@ -634,7 +634,24 @@ export class CheckpointManager {
     const ids = snapshot.completedExecutionIds;
     if (!Array.isArray(ids) || ids.length === 0) return;
 
-    const completedSet = new Set(state.completedTasks);
+    // Build the set of completed tasks. If completedTasks is empty (legacy
+    // checkpoints that never called completeTask()), derive the set from
+    // the flow checkpoint's own commit entries so we don't discard all progress.
+    let completedSet = new Set(state.completedTasks);
+    if (completedSet.size === 0) {
+      const TASK_ID_RE = /\/(task-[^/]+)\/[^/]+\/commit$/;
+      for (const id of ids) {
+        const m = TASK_ID_RE.exec(id);
+        if (m) completedSet.add(m[1]!);
+      }
+      // Back-fill completedTasks so downstream logic stays consistent.
+      if (completedSet.size > 0) {
+        state.completedTasks = [...completedSet];
+        this.logger.info(
+          `Back-filled ${completedSet.size} completed task(s) from Phase 4 flow checkpoint commit entries`,
+        );
+      }
+    }
     if (completedSet.size === ids.length) return; // all tasks completed, nothing to filter
 
     const filtered = ids.filter((id: string) => {
diff --git a/src/core/lore-index-settings.ts b/src/core/lore-index-settings.ts
new file mode 100644
index 0000000..6238140
--- /dev/null
+++ b/src/core/lore-index-settings.ts
@@ -0,0 +1,113 @@
+import type { EffectiveLspSettings, EffectiveScipSettings } from '@jafreck/lore';
+import type { MigrationConfig } from '../config/schema.js';
+
+type KbIndexConfig = MigrationConfig['options']['kbIndex'];
+type LspServerOverride = { command: string; args?: string[] };
+
+const DEFAULT_LSP_REQUEST_TIMEOUT_MS = 5_000;
+const DEFAULT_SCIP_TIMEOUT_MS = 120_000;
+
+// Lore's programmatic API expects fully-effective settings, but the helper
+// functions that build those defaults are not part of the public export surface.
+// Mirror the 0.4.0 defaults here so AAMF can always pass the new API shape.
+const DEFAULT_LSP_SERVER_REGISTRY: EffectiveLspSettings['servers'] = {
+  c: { command: 'clangd', args: [] },
+  rust: { command: 'rust-analyzer', args: [] },
+  python: { command: 'pyright-langserver', args: ['--stdio'] },
+  cpp: { command: 'clangd', args: [] },
+  typescript: { command: 'typescript-language-server', args: ['--stdio'] },
+  javascript: { command: 'typescript-language-server', args: ['--stdio'] },
+  go: { command: 'gopls', args: [] },
+  java: { command: 'jdtls', args: [] },
+  csharp: { command: 'csharp-ls', args: [] },
+  ruby: { command: 'solargraph', args: ['stdio'] },
+  php: { command: 'intelephense', args: ['--stdio'] },
+  swift: { command: 'sourcekit-lsp', args: [] },
+  kotlin: { command: 'kotlin-language-server', args: [] },
+  scala: { command: 'metals', args: [] },
+  lua: { command: 'lua-language-server', args: [] },
+  bash: { command: 'bash-language-server', args: ['start'] },
+  elixir: { command: 'elixir-ls', args: [] },
+  zig: { command: 'zls', args: [] },
+  ocaml: { command: 'ocamllsp', args: [] },
+  haskell: { command: 'haskell-language-server-wrapper', args: ['--lsp'] },
+  julia: {
+    command: 'julia',
+    args: ['--startup-file=no', '--history-file=no', '--quiet', '--eval', 'using LanguageServer, SymbolServer; runserver()'],
+  },
+  elm: { command: 'elm-language-server', args: [] },
+  objc: { command: 'clangd', args: [] },
+};
+
+const DEFAULT_SCIP_INDEXER_REGISTRY: EffectiveScipSettings['indexers'] = {
+  typescript: { command: 'scip-typescript', args: ['index', '--output', '{output}'] },
+  python: { command: 'scip-python', args: ['index', '.', '--project-name', 'project', '--output', '{output}'] },
+  java: { command: 'scip-java', args: ['index', '--output', '{output}'] },
+  scala: { command: 'scip-java', args: ['index', '--output', '{output}'] },
+  kotlin: { command: 'scip-java', args: ['index', '--output', '{output}'] },
+  rust: { command: 'rust-analyzer', args: ['scip', '.'] },
+  c: { command: 'scip-clang', args: ['--compdb-path={compdb}', '--index-output-path={output}'] },
+  cpp: { command: 'scip-clang', args: ['--compdb-path={compdb}', '--index-output-path={output}'] },
+  csharp: { command: 'scip-dotnet', args: ['index', '.', '--output', '{output}'] },
+  ruby: { command: 'scip-ruby', args: ['--output', '{output}'] },
+  php: { command: 'scip-php', args: ['index', '--output', '{output}'] },
+  go: { command: 'scip-go', args: [] },
+  dart: { command: 'scip-dart', args: ['index', '--output', '{output}'] },
+};
+
+export interface LoreIndexSettings {
+  lsp: EffectiveLspSettings;
+  scip: EffectiveScipSettings;
+}
+
+function cloneLspServerRegistry(registry: EffectiveLspSettings['servers']): EffectiveLspSettings['servers'] {
+  return Object.fromEntries(
+    Object.entries(registry).map(([language, server]) => [
+      language,
+      { command: server.command, args: [...server.args] },
+    ]),
+  );
+}
+
+function cloneScipIndexerRegistry(registry: EffectiveScipSettings['indexers']): EffectiveScipSettings['indexers'] {
+  return Object.fromEntries(
+    Object.entries(registry).map(([language, indexer]) => [
+      language,
+      {
+        command: indexer.command,
+        args: [...indexer.args],
+        ...(indexer.cwd ? { cwd: indexer.cwd } : {}),
+      },
+    ]),
+  );
+}
+
+function mergeLspServerOverrides(
+  overrides: Record<string, LspServerOverride> | undefined,
+): EffectiveLspSettings['servers'] {
+  const merged = cloneLspServerRegistry(DEFAULT_LSP_SERVER_REGISTRY);
+  for (const [language, override] of Object.entries(overrides ?? {})) {
+    const base = merged[language];
+    merged[language] = {
+      command: override.command ?? base?.command ?? '',
+      args: override.args ?? base?.args ?? [],
+    };
+  }
+  return merged;
+}
+
+export function buildLoreIndexSettings(kbIndex: KbIndexConfig | undefined): LoreIndexSettings {
+  return {
+    lsp: {
+      enabled: kbIndex?.lsp?.enabled ?? false,
+      requestTimeoutMs: kbIndex?.lsp?.requestTimeoutMs ?? DEFAULT_LSP_REQUEST_TIMEOUT_MS,
+      servers: mergeLspServerOverrides(kbIndex?.lsp?.servers),
+    },
+    scip: {
+      enabled: true,
+      timeoutMs: DEFAULT_SCIP_TIMEOUT_MS,
+      indexers: cloneScipIndexerRegistry(DEFAULT_SCIP_INDEXER_REGISTRY),
+      indexDir: null,
+    },
+  };
+}
\ No newline at end of file
diff --git a/src/core/runtime.ts b/src/core/runtime.ts
index 6bce851..122ac52 100644
--- a/src/core/runtime.ts
+++ b/src/core/runtime.ts
@@ -21,6 +21,7 @@ import { ContextBuilder } from '../agents/context-builder.js';
 import { MetricsCollector } from '../observability/metrics-collector.js';
 import { ReportGenerator } from '../observability/report-generator.js';
 import { TargetIndexer } from './target-indexer.js';
+import { buildLoreIndexSettings } from './lore-index-settings.js';
 import { FlowRunner, type FlowRunnerOptions } from '@cadre-dev/framework/flow';
 import { migrationFlow, AamfFlowCheckpointAdapter, buildFlowUpToPhase, nodeIdToPhase } from '../flow/index.js';
 import { MigrationError } from '../flow/steps/shared.js';
@@ -247,7 +248,13 @@ export class MigrationRuntime {
     const gitLimiter = pLimit(1);
 
     // Target codebase indexer
-    const targetIndexer = new TargetIndexer(this.paths.kbTargetDbFile, this.config.target.outputPath, this.logger);
+    const loreIndexSettings = buildLoreIndexSettings(this.config.options.kbIndex);
+    const targetIndexer = new TargetIndexer(
+      this.paths.kbTargetDbFile,
+      this.config.target.outputPath,
+      this.logger,
+      loreIndexSettings,
+    );
 
     // If the target DB already exists (resume), mark the indexer as built.
     if (await fileExists(this.paths.kbTargetDbFile)) {
diff --git a/src/core/target-indexer.ts b/src/core/target-indexer.ts
index 341fb89..9aabe2b 100644
--- a/src/core/target-indexer.ts
+++ b/src/core/target-indexer.ts
@@ -11,19 +11,36 @@
  */
 
 import type { Logger } from '../logging/logger.js';
+import { buildLoreIndexSettings, type LoreIndexSettings } from './lore-index-settings.js';
 
 export class TargetIndexer {
   private readonly dbPath: string;
   private readonly rootDir: string;
   private readonly logger: Logger;
+  private readonly indexSettings: LoreIndexSettings;
   private built = false;
   private building = false;
   private onFirstBuild?: () => Promise<void>;
 
-  constructor(dbPath: string, rootDir: string, logger: Logger) {
+  constructor(
+    dbPath: string,
+    rootDir: string,
+    logger: Logger,
+    indexSettings: LoreIndexSettings = buildLoreIndexSettings(undefined),
+  ) {
     this.dbPath = dbPath;
     this.rootDir = rootDir;
     this.logger = logger;
+    this.indexSettings = indexSettings;
+  }
+
+  private createBuilder(lore: typeof import('@jafreck/lore')): InstanceType<typeof lore.IndexBuilder> {
+    return new lore.IndexBuilder(
+      this.dbPath,
+      { rootDir: this.rootDir },
+      undefined,
+      this.indexSettings,
+    );
   }
 
   /** Register a callback that fires once after the first build/update completes. */
@@ -34,7 +51,7 @@ export class TargetIndexer {
   /** Full build of the target index from scratch. */
   async build(): Promise<void> {
     const lore = await import('@jafreck/lore');
-    const builder = new lore.IndexBuilder(this.dbPath, { rootDir: this.rootDir });
+    const builder = this.createBuilder(lore);
     await builder.build();
     this.built = true;
     this.logger.info('Target index built');
@@ -54,7 +71,7 @@ export class TargetIndexer {
       if (this.building) return;
       this.building = true;
       // First update — do a full build to establish the schema.
-      const builder = new lore.IndexBuilder(this.dbPath, { rootDir: this.rootDir });
+      const builder = this.createBuilder(lore);
       await builder.build();
       this.built = true;
       this.building = false;
@@ -64,9 +81,16 @@ export class TargetIndexer {
         this.onFirstBuild = undefined;
       }
     } else {
-      const builder = new lore.IndexBuilder(this.dbPath, { rootDir: this.rootDir });
-      await builder.update(changedFiles);
-      this.logger.debug(`Target index updated for ${changedFiles.length} file(s)`);
+      const builder = this.createBuilder(lore);
+      if (this.indexSettings.lsp.enabled) {
+        await builder.update(changedFiles);
+        this.logger.debug(`Target index updated for ${changedFiles.length} file(s)`);
+      } else {
+        await builder.baselineRebuild();
+        this.logger.debug(
+          `Target index baseline rebuilt for ${changedFiles.length} changed file(s) because LSP is disabled`,
+        );
+      }
     }
   }
 
diff --git a/src/flow/steps/kb-indexing.ts b/src/flow/steps/kb-indexing.ts
index 8d0aa6b..36abed2 100644
--- a/src/flow/steps/kb-indexing.ts
+++ b/src/flow/steps/kb-indexing.ts
@@ -14,6 +14,7 @@ import type { MigrationFlowContext } from '../context.js';
 import type { PhaseResult } from '../../agents/types.js';
 import { assertPhaseSuccess } from './shared.js';
 import { startKbServer } from './kb-server-lifecycle.js';
+import { buildLoreIndexSettings } from '../../core/lore-index-settings.js';
 import { fileExists } from '../../util/fs.js';
 
 const loadLore = () => import('@jafreck/lore');
@@ -102,32 +103,23 @@ export async function buildKbIndex(
     }
   }
 
-  // ── LSP settings ──
+  const loreIndexSettings = buildLoreIndexSettings(ctx.config.options.kbIndex);
   const lspConfig = ctx.config.options.kbIndex?.lsp;
-  const lspSettings = lspConfig?.enabled ? {
-    enabled: true as const,
-    requestTimeoutMs: lspConfig.requestTimeoutMs ?? 5000,
-    servers: lspConfig.servers
-      ? Object.fromEntries(
-          Object.entries(lspConfig.servers).map(([lang, srv]) => [
-            lang, { command: srv.command, args: srv.args ?? [] },
-          ]),
-        )
-      : {},
-  } : undefined;
-
-  if (lspSettings) {
+
+  if (loreIndexSettings.lsp.enabled) {
     ctx.logger.info(
-      `LSP enabled (timeout: ${lspSettings.requestTimeoutMs}ms` +
-      (Object.keys(lspSettings.servers).length > 0
-        ? `, servers: ${Object.keys(lspSettings.servers).join(', ')}` : '') + ')',
+      `LSP enabled (timeout: ${loreIndexSettings.lsp.requestTimeoutMs}ms` +
+      (Object.keys(lspConfig?.servers ?? {}).length > 0
+        ? `, overrides: ${Object.keys(lspConfig?.servers ?? {}).join(', ')}` : '') + ')',
     );
-    for (const [lang, srv] of Object.entries(lspSettings.servers)) {
+    for (const [lang, srv] of Object.entries(lspConfig?.servers ?? {})) {
       try { execFileSync('which', [srv.command], { stdio: 'pipe' }); }
       catch { ctx.logger.warn(`LSP server '${srv.command}' for '${lang}' not found on PATH`); }
     }
   }
 
+  ctx.logger.info(`SCIP enabled (timeout: ${loreIndexSettings.scip.timeoutMs}ms)`);
+
   // ── Logger init ──
   const loreLogLevel = ctx.config.options.kbIndex?.logLevel ?? 'debug';
   lore.initLogger({
@@ -135,7 +127,7 @@ export async function buildKbIndex(
     logFile: ctx.paths.loreLogFile,
   });
 
-  const builder = new lore.IndexBuilder(kbDbPath, walkerConfig, ctx.embedder, { lsp: lspSettings });
+  const builder = new lore.IndexBuilder(kbDbPath, walkerConfig, ctx.embedder, loreIndexSettings);
 
   // ── Retry loop ──
   const maxAttempts = ctx.config.options.maxRetriesPerTask;
@@ -161,7 +153,7 @@ export async function buildKbIndex(
         ctx.logger.warn(
           `KB index build still running after ${Math.round(halfTimeout / 1000)}s ` +
           `(timeout: ${Math.round(timeout / 1000)}s)` +
-          (lspSettings ? ' — LSP server may still be indexing.' : ''),
+          (loreIndexSettings.lsp.enabled ? ' — LSP server may still be indexing.' : ''),
         );
       }, halfTimeout),
     );
@@ -173,7 +165,7 @@ export async function buildKbIndex(
         new Promise<never>((_, reject) =>
           setTimeout(() => {
             clearHeartbeat();
-            const msg = lspSettings
+            const msg = loreIndexSettings.lsp.enabled
               ? `KB index timed out after ${Math.round(timeout / 1000)}s — LSP may be stalled.`
               : `KB index timed out after ${Math.round(timeout / 1000)}s`;
             reject(new Error(msg));
diff --git a/src/flow/steps/migration.ts b/src/flow/steps/migration.ts
index 55adc41..cfa81c3 100644
--- a/src/flow/steps/migration.ts
+++ b/src/flow/steps/migration.ts
@@ -240,6 +240,7 @@ async function runCommitSubstep(
   ctx: MigrationFlowContext, task: MigrationTask,
 ): Promise<void> {
   await commitForAgent(ctx, 'code-migrator', 5, task.id, task.name);
+  await ctx.checkpoint.completeTask(task.id);
 }
 
 async function runTargetIndexSubstep(
@@ -552,6 +553,7 @@ function buildPerTaskFlow(
         await ctx.progress.updateTask(task.id, 'completed', { sourceFiles: task.sourceFiles, targetFiles: task.targetFiles });
         ctx.logger.event({ type: 'task-completed', taskId: task.id, name: task.name, duration: 0 });
         await commitForTask(c.context, task);
+        await ctx.checkpoint.completeTask(task.id);
       },
     }));
   }
diff --git a/tests/agents/plan-parser.test.ts b/tests/agents/plan-parser.test.ts
index 77b5d2c..55862ef 100644
--- a/tests/agents/plan-parser.test.ts
+++ b/tests/agents/plan-parser.test.ts
@@ -557,6 +557,31 @@ intermediate text
       }
     });
 
+    it('should normalize legacy success status and notes arrays', () => {
+      const stdout = `\`\`\`aamf-json
+{"status":"success","written":["strategy.md","compilation-units.json"],"notes":["First note","Second note"]}
+\`\`\``;
+      const result = parseAamfOutput(stdout, AamfOutputBase);
+      expect(result.parsed).toBe(true);
+      if (result.parsed) {
+        expect(result.data.status).toBe('completed');
+        expect(result.data.notes).toBe('First note\nSecond note');
+        expect((result.data as Record<string, unknown>).outputFiles).toEqual([
+          'strategy.md',
+          'compilation-units.json',
+        ]);
+      }
+    });
+
+    it('should normalize needs_review status alias', () => {
+      const stdout = '```aamf-json\n{"status":"needs_review"}\n```';
+      const result = parseAamfOutput(stdout, MigrationPlannerSchema);
+      expect(result.parsed).toBe(true);
+      if (result.parsed) {
+        expect(result.data.status).toBe('needs-review');
+      }
+    });
+
     it('should handle CRLF line endings in the fenced block', () => {
       const stdout = '```aamf-json\r\n{"status":"completed"}\r\n```';
       const result = parseAamfOutput(stdout, AdjudicatorSchema);
diff --git a/tests/core/checkpoint.test.ts b/tests/core/checkpoint.test.ts
index c9199ee..de441cd 100644
--- a/tests/core/checkpoint.test.ts
+++ b/tests/core/checkpoint.test.ts
@@ -1038,6 +1038,79 @@ describe('CheckpointManager', () => {
     expect(resumed.blockedTasks).toEqual([]);
   });
 
+  it('should back-fill completedTasks from Phase 4 commit entries when completedTasks is empty', async () => {
+    const { writeJson } = await import('../../src/util/fs.js');
+    const checkpoint = {
+      projectName: 'test-backfill-resume',
+      version: 1,
+      currentPhase: 4,
+      currentTask: null,
+      completedPhases: [0, 1, 2, 3],
+      completedTasks: [],  // BUG: completeTask was never called
+      failedTasks: [{ taskId: 'task-bad-0', attempts: 2, lastError: 'Exit code: null', recoveryAttempted: false }],
+      blockedTasks: [],
+      phaseOutputs: {},
+      tokenUsage: { total: 0, byPhase: {}, byAgent: {} },
+      startedAt: new Date().toISOString(),
+      lastCheckpoint: new Date().toISOString(),
+      resumeCount: 0,
+      cumulativeDurationMs: 0,
+      completedTaskDurationsMs: [],
+      metricsCount: 0,
+      __flowCheckpoint: {
+        flowId: 'aamf-migration',
+        status: 'running',
+        startedAt: new Date().toISOString(),
+        updatedAt: new Date().toISOString(),
+        completedExecutionIds: ['aamf-migration/kb-index'],
+        outputs: {},
+        executionOutputs: {},
+      },
+      __phase4FlowCheckpoint: {
+        flowId: 'phase-4-sync-epoch',
+        status: 'running',
+        startedAt: new Date().toISOString(),
+        updatedAt: new Date().toISOString(),
+        completedExecutionIds: [
+          'phase-4-sync-epoch/epoch-0-start',
+          // Committed task A — all substeps present
+          'phase-4-sync-epoch/epoch-0-tasks-batch-0/task-ok-0/task-ok-0/migrate',
+          'phase-4-sync-epoch/epoch-0-tasks-batch-0/task-ok-0/task-ok-0/commit',
+          'phase-4-sync-epoch/epoch-0-tasks-batch-0/task-ok-0/task-ok-0/target-index',
+          'phase-4-sync-epoch/epoch-0-tasks-batch-0/task-ok-0/task-ok-0/parity',
+          // Committed task B
+          'phase-4-sync-epoch/epoch-0-tasks-batch-1/task-ok-1/task-ok-1/migrate',
+          'phase-4-sync-epoch/epoch-0-tasks-batch-1/task-ok-1/task-ok-1/commit',
+          'phase-4-sync-epoch/epoch-0-tasks-batch-1/task-ok-1/task-ok-1/parity',
+          // Failed task — migrated but no commit
+          'phase-4-sync-epoch/epoch-0-tasks-batch-0/task-bad-0/task-bad-0/migrate',
+        ],
+        outputs: {},
+        executionOutputs: {},
+      },
+    };
+    await ensureDir(join(tempDir, 'state'));
+    await writeJson(join(tempDir, 'state', 'checkpoint.json'), checkpoint);
+
+    const manager3 = new CheckpointManager(tempDir, logger);
+    const resumed = await manager3.load('test-backfill-resume');
+
+    // completedTasks should be back-filled from commit entries
+    expect(resumed.completedTasks).toContain('task-ok-0');
+    expect(resumed.completedTasks).toContain('task-ok-1');
+    expect(resumed.completedTasks).not.toContain('task-bad-0');
+
+    // Phase 4 flow checkpoint should preserve committed task entries
+    const p4fc = resumed.__phase4FlowCheckpoint as Record<string, unknown>;
+    const p4Ids = p4fc.completedExecutionIds as string[];
+    expect(p4Ids).toContain('phase-4-sync-epoch/epoch-0-start');
+    expect(p4Ids).toContain('phase-4-sync-epoch/epoch-0-tasks-batch-0/task-ok-0/task-ok-0/migrate');
+    expect(p4Ids).toContain('phase-4-sync-epoch/epoch-0-tasks-batch-0/task-ok-0/task-ok-0/commit');
+    expect(p4Ids).toContain('phase-4-sync-epoch/epoch-0-tasks-batch-1/task-ok-1/task-ok-1/migrate');
+    // Failed task entries should be removed
+    expect(p4Ids).not.toContain('phase-4-sync-epoch/epoch-0-tasks-batch-0/task-bad-0/task-bad-0/migrate');
+  });
+
   it('should not alter flow checkpoint when status is not failed', async () => {
     const { writeJson } = await import('../../src/util/fs.js');
     const checkpoint = {
diff --git a/tests/core/lore-index-settings.test.ts b/tests/core/lore-index-settings.test.ts
new file mode 100644
index 0000000..b7fccf6
--- /dev/null
+++ b/tests/core/lore-index-settings.test.ts
@@ -0,0 +1,33 @@
+import { describe, expect, it } from 'vitest';
+import { buildLoreIndexSettings } from '../../src/core/lore-index-settings.js';
+
+describe('buildLoreIndexSettings', () => {
+  it('always enables SCIP with Lore 0.4 defaults', () => {
+    const settings = buildLoreIndexSettings(undefined);
+
+    expect(settings.scip.enabled).toBe(true);
+    expect(settings.scip.timeoutMs).toBe(120_000);
+    expect(settings.scip.indexDir).toBeNull();
+    expect(settings.scip.indexers.c.command).toBe('scip-clang');
+    expect(settings.scip.indexers.rust.args).toEqual(['scip', '.']);
+  });
+
+  it('keeps LSP opt-in and merges custom server overrides', () => {
+    const kbIndex = {
+      lsp: {
+        enabled: true,
+        requestTimeoutMs: 9_000,
+        servers: {
+          c: { command: 'clangd', args: ['--compile-commands-dir=build'] },
+        },
+      },
+    } satisfies NonNullable<Parameters<typeof buildLoreIndexSettings>[0]>;
+
+    const settings = buildLoreIndexSettings(kbIndex);
+
+    expect(settings.lsp.enabled).toBe(true);
+    expect(settings.lsp.requestTimeoutMs).toBe(9_000);
+    expect(settings.lsp.servers.c.args).toEqual(['--compile-commands-dir=build']);
+    expect(settings.lsp.servers.rust.command).toBe('rust-analyzer');
+  });
+});
\ No newline at end of file
diff --git a/tests/core/target-indexer-lore-settings.test.ts b/tests/core/target-indexer-lore-settings.test.ts
new file mode 100644
index 0000000..599074b
--- /dev/null
+++ b/tests/core/target-indexer-lore-settings.test.ts
@@ -0,0 +1,58 @@
+import { describe, expect, it, vi, beforeEach } from 'vitest';
+import { TargetIndexer } from '../../src/core/target-indexer.js';
+import { buildLoreIndexSettings } from '../../src/core/lore-index-settings.js';
+import { createSilentLogger } from '../helpers/mocks.js';
+
+const builderMethods = vi.hoisted(() => ({
+  build: vi.fn().mockResolvedValue(undefined),
+  update: vi.fn().mockResolvedValue(undefined),
+  baselineRebuild: vi.fn().mockResolvedValue(undefined),
+}));
+
+vi.mock('@jafreck/lore', () => ({
+  IndexBuilder: class {
+    build = builderMethods.build;
+    update = builderMethods.update;
+    baselineRebuild = builderMethods.baselineRebuild;
+  },
+}));
+
+describe('TargetIndexer Lore integration', () => {
+  beforeEach(() => {
+    builderMethods.build.mockClear();
+    builderMethods.update.mockClear();
+    builderMethods.baselineRebuild.mockClear();
+  });
+
+  it('uses baseline rebuilds for follow-up updates when LSP is disabled', async () => {
+    const logger = createSilentLogger(process.cwd());
+    const indexer = new TargetIndexer(
+      '/tmp/aamf-target.db',
+      '/tmp/aamf-target-root',
+      logger,
+      buildLoreIndexSettings(undefined),
+    );
+
+    indexer.markBuilt();
+    await indexer.updateForFiles(['/tmp/aamf-target-root/lib.rs']);
+
+    expect(builderMethods.update).not.toHaveBeenCalled();
+    expect(builderMethods.baselineRebuild).toHaveBeenCalledTimes(1);
+  });
+
+  it('uses overlay updates when LSP is enabled', async () => {
+    const logger = createSilentLogger(process.cwd());
+    const indexer = new TargetIndexer(
+      '/tmp/aamf-target.db',
+      '/tmp/aamf-target-root',
+      logger,
+      buildLoreIndexSettings({ lsp: { enabled: true } }),
+    );
+
+    indexer.markBuilt();
+    await indexer.updateForFiles(['/tmp/aamf-target-root/lib.rs']);
+
+    expect(builderMethods.update).toHaveBeenCalledTimes(1);
+    expect(builderMethods.baselineRebuild).not.toHaveBeenCalled();
+  });
+});
\ No newline at end of file
diff --git a/tests/core/task-graph-builder.test.ts b/tests/core/task-graph-builder.test.ts
index 4724e10..9c9a961 100644
--- a/tests/core/task-graph-builder.test.ts
+++ b/tests/core/task-graph-builder.test.ts
@@ -36,7 +36,8 @@ function createTestDb(dbPath: string): Database.Database {
       start_line INTEGER NOT NULL, end_line INTEGER NOT NULL,
       signature TEXT, doc_comment TEXT,
       resolved_type_signature TEXT, resolved_return_type TEXT,
-      definition_uri TEXT, definition_path TEXT
+      definition_uri TEXT, definition_path TEXT,
+      parent_symbol_id INTEGER REFERENCES symbols(id)
     );
     CREATE TABLE IF NOT EXISTS symbol_refs (
       id INTEGER PRIMARY KEY AUTOINCREMENT,
diff --git a/tests/fixtures/zstd-c-project/migration.config.json b/tests/fixtures/zstd-c-project/migration.config.json
index ddd5998..0509863 100644
--- a/tests/fixtures/zstd-c-project/migration.config.json
+++ b/tests/fixtures/zstd-c-project/migration.config.json
@@ -2,10 +2,10 @@
   "projectName": "zstd-to-rust",
   "guidance": [
     "Do NOT use any existing Rust crates that wrap the C implementation (e.g. zstd, zstd-safe, zstd-sys, lz4-sys). Write a pure native Rust port of the C source code.",
-    "Do NOT use FFI, bindgen, or any C interop. All code must be idiomatic safe Rust.",
-    "All code must be safe Rust. Do NOT use `unsafe` blocks, `unsafe fn`, raw pointers (`*const`, `*mut`), or `core::ffi::c_void`. Use slices (`&[u8]`, `&mut [u8]`), Vec, iterators, and Rust's standard byte-order methods (e.g. `u32::from_le_bytes`, `to_be_bytes`) instead of pointer casts and manual memory access. If a C pattern seems to require unsafe, find the safe Rust equivalent — it almost always exists.",
+    "Do NOT use bindgen or delegate to the original C implementation through FFI. If a platform or OS boundary truly has no safe Rust equivalent, a narrowly-scoped Rust-side ABI shim is allowed only at the leaf boundary, with the rest of the port remaining native Rust.",
+    "Prefer safe Rust everywhere. You may use audited `unsafe` blocks, `unsafe fn`, raw pointers (`*const`, `*mut`), or `core::ffi::c_void` only when no safe equivalent exists and the behavior is required for parity. Keep unsafe localized to the smallest possible boundary, document the invariant being relied on, and expose a safe API to the rest of the code.",
     "Preserve the algorithmic logic (same algorithmic steps, same data flow) so the port is auditable against the C reference — but use idiomatic Rust types and APIs. The algorithm should be recognizable, not the function signatures or pointer patterns.",
-    "Prefer correctness and safety over micro-optimization. It is acceptable for the Rust port to be slightly slower than the C original if the alternative is unsafe code. Do not use unsafe for performance reasons."
+    "Prefer correctness and safety over micro-optimization. It is acceptable for the Rust port to be slightly slower than the C original if the alternative is broader unsafe code. Do not use unsafe for convenience or performance reasons; if unsafe is used at all, it must be to preserve required behavior at a constrained boundary."
   ],
   "source": {
     "path": "./zstd-src/zstd-1.5.7",
@@ -74,7 +74,7 @@
         "enabled": false
       },
       "lsp": {
-        "enabled": true,
+        "enabled": false,
         "servers": {
           "c": { "command": "clangd", "args": ["--compile-commands-dir=zstd-src/zstd-1.5.7/build"] }
         }
diff --git a/tests/lore/kb-search-tool.test.ts b/tests/lore/kb-search-tool.test.ts
index e510669..23df762 100644
--- a/tests/lore/kb-search-tool.test.ts
+++ b/tests/lore/kb-search-tool.test.ts
@@ -105,8 +105,9 @@ describe('kb search tool handler', () => {
     const result = await handler(db, { query: 'concept', mode: 'semantic' }, embedder as any);
 
     expect(result.mode_used).toBe('semantic');
-    // v0.2.1 re-sorts semantic results ascending by score
-    expect(result.results.map((r: any) => r.symbol_id)).toEqual([2, 3]);
+    // Semantic results are returned in the order provided by the DB query;
+    // the lore library no longer re-sorts them.
+    expect(result.results.map((r: any) => r.symbol_id)).toEqual([3, 2]);
     expect(embedder.embed).toHaveBeenCalledWith(['concept']);
   });
 
diff --git a/tests/lore/kb-server.test.ts b/tests/lore/kb-server.test.ts
index ad28ab0..294d7a2 100644
--- a/tests/lore/kb-server.test.ts
+++ b/tests/lore/kb-server.test.ts
@@ -65,6 +65,15 @@ beforeAll(async () => {
       } catch {
         // FTS table may not exist in all Lore versions — non-fatal.
       }
+      // Populate symbol_metrics so the metrics handler test works.
+      try {
+        rwDb.prepare(
+          `INSERT INTO symbol_metrics (symbol_id, line_count, param_count, cyclomatic, max_nesting)
+           VALUES (?, 20, 0, 1, 0)`,
+        ).run(symId);
+      } catch {
+        // symbol_metrics may not exist — non-fatal.
+      }
     }
   }
   rwDb.close();