feat(FN-4062): add global thinking log setting to persist agent reasoning a

Adds a global `thinkingLogEnabled` setting that gates AI thinking log persistence across the engine (executor, reviewer, merger, triage, step-session) and exposes the control in the dashboard Settings modal, with tests verifying settings parity and modal behavior.

Fusion-Task-Id: FN-4062

packages/engine/src/__tests__/agent-logger.test.ts

@@ -269,7 +269,7 @@ describe("AgentLogger", () => {
 
   // ── Thinking buffer/flush ────────────────────────────────────────
 
-  it("buffers thinking deltas and flushes on timer", async () => {
+  it("skips thinking entries by default", async () => {
     const store = createMockStore();
     const logger = new AgentLogger({
       store,
@@ -279,12 +279,30 @@ describe("AgentLogger", () => {
       flushIntervalMs: 500,
     });
 
+    logger.onThinking("thought 1 ");
+    logger.onThinking("thought 2");
+    await vi.advanceTimersByTimeAsync(500);
+
+    expect(store.appendAgentLog).not.toHaveBeenCalled();
+  });
+
+  it("buffers thinking deltas and flushes on timer when enabled", async () => {
+    const store = createMockStore();
+    const logger = new AgentLogger({
+      store,
+      taskId: "FN-011A",
+      agent: "executor",
+      persistAgentThinkingLog: true,
+      flushSizeBytes: 1024,
+      flushIntervalMs: 500,
+    });
+
     logger.onThinking("thought 1 ");
     logger.onThinking("thought 2");
     expect(store.appendAgentLog).not.toHaveBeenCalled();
 
     await vi.advanceTimersByTimeAsync(500);
-    expect(store.appendAgentLog).toHaveBeenCalledWith("FN-011", "thought 1 thought 2", "thinking", undefined, "executor");
+    expect(store.appendAgentLog).toHaveBeenCalledWith("FN-011A", "thought 1 thought 2", "thinking", undefined, "executor");
   });
 
   it("flushes thinking on size threshold", async () => {
@@ -293,6 +311,7 @@ describe("AgentLogger", () => {
       store,
       taskId: "FN-012",
       agent: "triage",
+      persistAgentThinkingLog: true,
       flushSizeBytes: 10,
     });
 
@@ -310,6 +329,7 @@ describe("AgentLogger", () => {
       store,
       taskId: "FN-013",
       agent: "reviewer",
+      persistAgentThinkingLog: true,
       flushSizeBytes: 1024,
     });
 
@@ -324,6 +344,7 @@ describe("AgentLogger", () => {
       store,
       taskId: "FN-014",
       agent: "executor",
+      persistAgentThinkingLog: true,
       flushSizeBytes: 1024,
     });
 
@@ -463,6 +484,7 @@ describe("AgentLogger", () => {
       const logger = new AgentLogger({
         store,
         taskId: "FN-2090-THINKING",
+        persistAgentThinkingLog: true,
         flushSizeBytes: 1,
       });
 

packages/engine/src/agent-heartbeat.ts

@@ -1890,6 +1890,7 @@ export class HeartbeatMonitor {
             appendLog: (entry) => this.store.appendRunLog(agentId, run.id, entry),
             agent: agent.role as AgentRole,
             persistAgentToolOutput: memorySettings?.persistAgentToolOutput,
+            persistAgentThinkingLog: memorySettings?.persistAgentThinkingLog,
           });
         } else if (taskId) {
           agentLogger = new AgentLogger({
@@ -1898,6 +1899,7 @@ export class HeartbeatMonitor {
             agent: agent.role as AgentRole,
             appendLog: (entry) => this.store.appendRunLog(agentId, run.id, entry),
             persistAgentToolOutput: memorySettings?.persistAgentToolOutput,
+            persistAgentThinkingLog: memorySettings?.persistAgentThinkingLog,
           });
         }
 

packages/engine/src/agent-logger.ts

@@ -46,6 +46,8 @@ export function summarizeToolArgs(name: string, args?: Record<string, unknown>):
 export interface AgentLoggerOptions {
   /** When false, omit `detail` payloads for tool entries while preserving the rows. */
   persistAgentToolOutput?: boolean;
+  /** When true, persist `thinking` rows. Default: false (skip thinking persistence). */
+  persistAgentThinkingLog?: boolean;
   /** The task store used to persist agent log entries (task-store mode). */
   store?: TaskStore;
   /** The task ID this logger is associated with (task-store mode). */
@@ -110,6 +112,7 @@ export class AgentLogger {
   private readonly externalToolCb?: (taskId: string, toolName: string) => void;
   private readonly log = createLogger("agent-logger");
   private readonly persistAgentToolOutput: boolean;
+  private readonly persistAgentThinkingLog: boolean;
 
   constructor(options: AgentLoggerOptions) {
     this.store = options.store;
@@ -121,6 +124,7 @@ export class AgentLogger {
     this.flushSizeBytes = options.flushSizeBytes ?? FLUSH_SIZE_BYTES;
     this.flushIntervalMs = options.flushIntervalMs ?? FLUSH_INTERVAL_MS;
     this.persistAgentToolOutput = options.persistAgentToolOutput !== false;
+    this.persistAgentThinkingLog = options.persistAgentThinkingLog === true;
 
     // Bind callbacks so they can be passed directly as function references
     this.onText = this.onText.bind(this);
@@ -149,6 +153,9 @@ export class AgentLogger {
    * as `type: "thinking"` entries, using the same size/timer pattern as `onText`.
    */
   onThinking(delta: string): void {
+    if (!this.persistAgentThinkingLog) {
+      return;
+    }
     this.thinkingBuffer += delta;
     if (this.thinkingBuffer.length >= this.flushSizeBytes) {
       if (this.thinkingFlushTimer) { clearTimeout(this.thinkingFlushTimer); this.thinkingFlushTimer = null; }
@@ -258,6 +265,9 @@ export class AgentLogger {
     if (this.thinkingBuffer.length === 0) return Promise.resolve();
     const chunk = this.thinkingBuffer;
     this.thinkingBuffer = "";
+    if (!this.persistAgentThinkingLog) {
+      return Promise.resolve();
+    }
     this.writeEntry(chunk, "thinking", undefined, `Failed to flush thinking buffer for ${this.taskId}`, true);
     return this.flushPendingEntries();
   }

packages/engine/src/executor.ts

@@ -3152,6 +3152,7 @@ export class TaskExecutor {
         taskId: task.id,
         agent: "executor",
         persistAgentToolOutput: settings.persistAgentToolOutput,
+        persistAgentThinkingLog: settings.persistAgentThinkingLog,
         onAgentText: (taskId, delta) => {
           lastAssistantText += delta;
           stuckDetector?.recordActivity(taskId);
@@ -4960,6 +4961,7 @@ ${feedback}
         taskId: task.id,
         agent: "executor",
         persistAgentToolOutput: settings.persistAgentToolOutput,
+        persistAgentThinkingLog: settings.persistAgentThinkingLog,
         onAgentText: this.options.onAgentText,
         onAgentTool: this.options.onAgentTool,
       });
@@ -5769,6 +5771,7 @@ and show an appropriate message to the user.\`
       taskId: task.id,
       agent: "reviewer",
       persistAgentToolOutput: settings.persistAgentToolOutput,
+      persistAgentThinkingLog: settings.persistAgentThinkingLog,
       onAgentText: (taskId, delta) => {
         this.options.onAgentText?.(taskId, delta);
       },

packages/engine/src/merger.ts

@@ -917,6 +917,7 @@ async function attemptInMergeVerificationFix(
       taskId,
       agent: "merger",
       persistAgentToolOutput: settings.persistAgentToolOutput,
+      persistAgentThinkingLog: settings.persistAgentThinkingLog,
       onAgentText: options.onAgentText,
       onAgentTool: options.onAgentTool,
     });
@@ -2026,6 +2027,7 @@ async function runAiAgentForAutostashConflict(params: {
     taskId,
     agent: "merger",
     persistAgentToolOutput: settings.persistAgentToolOutput,
+    persistAgentThinkingLog: settings.persistAgentThinkingLog,
     onAgentText: options.onAgentText
       ? (_id: string, delta: string) => options.onAgentText!(delta)
       : undefined,
@@ -2395,6 +2397,7 @@ async function runAiAgentForAutostashHardFail(params: {
     taskId,
     agent: "merger",
     persistAgentToolOutput: settings.persistAgentToolOutput,
+    persistAgentThinkingLog: settings.persistAgentThinkingLog,
     onAgentText: options.onAgentText
       ? (_id: string, delta: string) => options.onAgentText!(delta)
       : undefined,
@@ -4442,6 +4445,7 @@ You are assisting with a paused \`git pull --rebase\`.
     taskId,
     agent: "merger",
     persistAgentToolOutput: settings.persistAgentToolOutput,
+    persistAgentThinkingLog: settings.persistAgentThinkingLog,
     onAgentText: options?.onAgentText
       ? (_id, delta) => options.onAgentText?.(delta)
       : undefined,
@@ -7132,6 +7136,7 @@ async function runAiAgentForCommit(params: AiAgentParams): Promise<{ success: bo
     taskId,
     agent: "merger",
     persistAgentToolOutput: settings.persistAgentToolOutput,
+    persistAgentThinkingLog: settings.persistAgentThinkingLog,
     onAgentText: options.onAgentText
       ? (_id, delta) => options.onAgentText!(delta)
       : undefined,
@@ -7737,6 +7742,7 @@ If issues are found that need attention, describe them clearly and include concr
     taskId,
     agent: "merger",
     persistAgentToolOutput: settings.persistAgentToolOutput,
+    persistAgentThinkingLog: settings.persistAgentThinkingLog,
   });
 
   try {

packages/engine/src/reviewer.ts

@@ -351,6 +351,7 @@ export async function reviewStep(
           ? (_id, delta) => options.onText!(delta)
           : undefined,
         persistAgentToolOutput: liveSettings?.persistAgentToolOutput,
+        persistAgentThinkingLog: liveSettings?.persistAgentThinkingLog,
       })
     : null;
 

packages/engine/src/step-session-executor.ts

@@ -890,6 +890,7 @@ export class StepSessionExecutor {
           taskId: taskDetail.id,
           agent: "executor",
           persistAgentToolOutput: settings.persistAgentToolOutput,
+          persistAgentThinkingLog: settings.persistAgentThinkingLog,
         });
         let session: AgentSession | null = null;
 

packages/engine/src/triage.ts

@@ -913,6 +913,7 @@ export class TriageProcessor {
           taskId: task.id,
           agent: "triage",
           persistAgentToolOutput: settings.persistAgentToolOutput,
+          persistAgentThinkingLog: settings.persistAgentThinkingLog,
           onAgentText: (id, delta) => {
             stuckDetector?.recordActivity(task.id);
             this.options.onAgentText?.(id, delta);