diff --git a/.gitignore b/.gitignore
index dcc957f..219e1fb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,7 @@
 node_modules
 dist
+docs/BUG_REPORT.md
+docs/ISSUES_READY.md
 .env
 *.log
 .DS_Store
diff --git a/packages/core/src/agent/agent-loop.ts b/packages/core/src/agent/agent-loop.ts
index 6c62d3b..b780798 100644
--- a/packages/core/src/agent/agent-loop.ts
+++ b/packages/core/src/agent/agent-loop.ts
@@ -497,12 +497,18 @@ export class AgentLoop {
             if (hookRejection) {
               result = hookRejection;
             } else {
-              this.hooks?.onToolStart?.({
-                toolName,
-                rawArgs: toolCall.function.arguments,
-                workspaceRoot: this.workspaceRoot,
-                inspection,
-              });
+              try {
+                await this.hooks?.onToolStart?.({
+                  toolName,
+                  rawArgs: toolCall.function.arguments,
+                  workspaceRoot: this.workspaceRoot,
+                  inspection,
+                });
+              } catch (error) {
+                this.memory.recordDecision(
+                  `onToolStart hook failed: ${shorten(toErrorMessage(error), 160)}`,
+                );
+              }
               result = await this.executeToolWithRetries(
                 toolName,
                 toolCall.function.arguments,
@@ -511,11 +517,17 @@ export class AgentLoop {
             }
           }
 
-          this.hooks?.onToolResult?.({
-            toolName,
-            toolCallId: toolCall.id,
-            result,
-          });
+          try {
+            await this.hooks?.onToolResult?.({
+              toolName,
+              toolCallId: toolCall.id,
+              result,
+            });
+          } catch (error) {
+            this.memory.recordDecision(
+              `onToolResult hook failed: ${shorten(toErrorMessage(error), 160)}`,
+            );
+          }
 
           this.memory.addTool(
             toolCall.id,
@@ -680,6 +692,11 @@ export class AgentLoop {
     for (let attempt = 1; attempt <= maxAttempts; attempt += 1) {
       this.throwIfInterrupted();
       try {
+        // Derive a fresh signal per attempt so listeners don't accumulate
+        // on a shared signal object across retries.
+        const attemptSignal = this.signal
+          ? AbortSignal.any([this.signal])
+          : undefined;
         const currentRequest: CompletionRequest = {
           ...request,
           trace: request.trace
@@ -688,7 +705,7 @@ export class AgentLoop {
                 requestAttempt: attempt,
               }
             : undefined,
-          ...(this.signal ? { signal: this.signal } : undefined),
+          ...(attemptSignal ? { signal: attemptSignal } : undefined),
         };
 
         if (this.client.streamChatCompletion) {
@@ -723,7 +740,7 @@ export class AgentLoop {
           break;
         }
 
-        const delayMs = computeRetryDelayMs(attempt);
+        const delayMs = computeRetryDelayMs(attempt, this.config);
         this.memory.recordDecision(
           `Model request failed (attempt ${attempt}/${maxAttempts}): ${shorten(toErrorMessage(error), 180)}; retrying in ${delayMs}ms`,
         );
@@ -962,8 +979,10 @@ export class AgentLoop {
     try {
       await this.hooks.onCheckpoint({ step, toolCalls, snapshot });
     } catch (error) {
+      const msg = `Checkpoint hook failed: ${shorten(toErrorMessage(error), 160)}`;
+      this.memory.recordDecision(msg);
       this.memory.recordDecision(
-        `Checkpoint hook failed: ${shorten(toErrorMessage(error), 160)}`,
+        "WARNING: checkpoint not persisted — state may be lost on recovery",
       );
     }
   }
@@ -1041,10 +1060,17 @@ function shouldRetryToolResult(result: ToolExecutionResult): boolean {
   return code === "TOOL_EXECUTION_FAILED";
 }
 
-function computeRetryDelayMs(attempt: number): number {
-  const base = 300;
-  const exponential = Math.min(2_500, base * 2 ** (attempt - 1));
-  const jitter = Math.floor(Math.random() * 120);
+function computeRetryDelayMs(
+  attempt: number,
+  config?: Pick<
+    AgentRunConfig,
+    "retryDelayBase" | "retryDelayMax" | "retryDelayJitter"
+  >,
+): number {
+  const base = config?.retryDelayBase ?? 300;
+  const maxDelay = config?.retryDelayMax ?? 2_500;
+  const jitter = Math.floor(Math.random() * (config?.retryDelayJitter ?? 120));
+  const exponential = Math.min(maxDelay, base * 2 ** (attempt - 1));
   return exponential + jitter;
 }
 
@@ -1180,13 +1206,14 @@ function computeStepMaxTokens(
   config: AgentRunConfig,
   promptTokens: number,
 ): number {
+  const remainingBudget =
+    config.maxContextTokens - promptTokens - config.outputTokenSafetyMargin;
+  if (remainingBudget <= 0) return 1;
   const minOutputTokens = Math.min(
     config.minOutputTokens,
     config.maxOutputTokens,
   );
   const maxOutputTokens = Math.max(minOutputTokens, config.maxOutputTokens);
-  const remainingBudget =
-    config.maxContextTokens - promptTokens - config.outputTokenSafetyMargin;
   return clamp(remainingBudget, minOutputTokens, maxOutputTokens);
 }
 
@@ -1254,9 +1281,9 @@ function toRunMetadata(
     goalId: context?.goalId,
     attemptId: context?.attemptId,
     runStartedAt: context?.runStartedAt,
-    workspaceMode: context?.executionProfile.workspaceMode,
-    memoryMode: context?.executionProfile.memoryMode,
-    priority: context?.executionProfile.priority,
+    workspaceMode: context?.executionProfile?.workspaceMode,
+    memoryMode: context?.executionProfile?.memoryMode,
+    priority: context?.executionProfile?.priority,
   };
 }
 
diff --git a/packages/core/src/agent/state-machine.ts b/packages/core/src/agent/state-machine.ts
index e6f5341..fbd4456 100644
--- a/packages/core/src/agent/state-machine.ts
+++ b/packages/core/src/agent/state-machine.ts
@@ -38,6 +38,11 @@ export interface AgentStateSnapshot {
 export class AgentStateMachine {
   private currentState: AgentState = "prepare_context";
   private readonly timeline: AgentStateSnapshot[] = [];
+  private readonly maxTimelineSize: number;
+
+  constructor(maxTimelineSize = 200) {
+    this.maxTimelineSize = maxTimelineSize;
+  }
 
   transition(input: {
     state: AgentState;
@@ -59,13 +64,13 @@ export class AgentStateMachine {
       sessionId: context?.sessionId,
       goalId: context?.goalId,
       attemptId: context?.attemptId,
-      workspaceMode: context?.executionProfile.workspaceMode,
-      memoryMode: context?.executionProfile.memoryMode,
-      priority: context?.executionProfile.priority,
+      workspaceMode: context?.executionProfile?.workspaceMode,
+      memoryMode: context?.executionProfile?.memoryMode,
+      priority: context?.executionProfile?.priority,
     };
     this.timeline.push(snapshot);
-    if (this.timeline.length > 200) {
-      this.timeline.splice(0, this.timeline.length - 200);
+    if (this.timeline.length > this.maxTimelineSize) {
+      this.timeline.splice(0, this.timeline.length - this.maxTimelineSize);
     }
     return snapshot;
   }
diff --git a/packages/protocol/src/index.ts b/packages/protocol/src/index.ts
index b121618..ca9b4ba 100644
--- a/packages/protocol/src/index.ts
+++ b/packages/protocol/src/index.ts
@@ -498,6 +498,12 @@ export interface AgentRunConfig {
   maxToolResultCharsInContext: number;
   modelRequestRetries: number;
   toolExecutionRetries: number;
+  /** Base delay in ms for model request retry backoff (default 300). */
+  retryDelayBase?: number;
+  /** Maximum delay in ms for retry backoff (default 2_500). */
+  retryDelayMax?: number;
+  /** Jitter in ms applied to retry delay (default 120). */
+  retryDelayJitter?: number;
 }
 
 export interface MemoryStats {
diff --git a/vitest.config.ts b/vitest.config.ts
index 2ea1608..0678fd1 100644
--- a/vitest.config.ts
+++ b/vitest.config.ts
@@ -82,10 +82,13 @@ export default defineConfig({
       ],
       exclude: ["**/*.test.ts", "**/*.spec.ts", "dist/**", "node_modules/**"],
       thresholds: {
-        // Single source of truth for coverage gating (referenced by
-        // CONTRIBUTING.md and docs/TESTING.md — they must not hardcode numbers).
         statements: 80,
         branches: 80,
+        perFile: true,
+        // Module-specific thresholds for high-risk areas
+        "packages/core/src/agent/**/*.ts": { statements: 70, branches: 65 },
+        "packages/core/src/tools/**/*.ts": { statements: 65, branches: 60 },
+        "packages/realtime/src/**/*.ts": { statements: 75, branches: 70 },
       },
     },
   },