Improve error handling and logging across worker services (#528)

* fix: prevent memory_session_id from equaling content_session_id

The bug: memory_session_id was initialized to contentSessionId as a
"placeholder for FK purposes". This caused the SDK resume logic to
inject memory agent messages into the USER's Claude Code transcript,
corrupting their conversation history.

Root cause:
- SessionStore.createSDKSession initialized memory_session_id = contentSessionId
- SDKAgent checked memorySessionId !== contentSessionId but this check
  only worked if the session was fetched fresh from DB

The fix:
- SessionStore: Initialize memory_session_id as NULL, not contentSessionId
- SDKAgent: Simple truthy check !!session.memorySessionId (NULL = fresh start)
- Database migration: Ran UPDATE to set memory_session_id = NULL for 1807
  existing sessions that had the bug

Also adds [ALIGNMENT] logging across the session lifecycle to help debug
session continuity issues:
- Hook entry: contentSessionId + promptNumber
- DB lookup: contentSessionId → memorySessionId mapping proof
- Resume decision: shows which memorySessionId will be used for resume
- Capture: logs when memorySessionId is captured from first SDK response

UI: Added "Alignment" quick filter button in LogsModal to show only
alignment logs for debugging session continuity.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor: improve error handling in worker-service.ts

- Fix GENERIC_CATCH anti-patterns by logging full error objects instead of just messages
- Add [ANTI-PATTERN IGNORED] markers for legitimate cases (cleanup, hot paths)
- Simplify error handling comments to be more concise
- Improve httpShutdown() error discrimination for ECONNREFUSED
- Reduce LARGE_TRY_BLOCK issues in initialization code

Part of anti-pattern cleanup plan (132 total issues)

* refactor: improve error logging in SearchManager.ts

- Pass full error objects to logger instead of just error.message
- Fixes PARTIAL_ERROR_LOGGING anti-patterns (10 instances)
- Better debugging visibility when Chroma queries fail

Part of anti-pattern cleanup (133 remaining)

* refactor: improve error logging across SessionStore and mcp-server

- SessionStore.ts: Fix error logging in column rename utility
- mcp-server.ts: Log full error objects instead of just error.message
- Improve error handling in Worker API calls and tool execution

Part of anti-pattern cleanup (133 remaining)

* Refactor hooks to streamline error handling and loading states

- Simplified error handling in useContextPreview by removing try-catch and directly checking response status.
- Refactored usePagination to eliminate try-catch, improving readability and maintaining error handling through response checks.
- Cleaned up useSSE by removing unnecessary try-catch around JSON parsing, ensuring clarity in message handling.
- Enhanced useSettings by streamlining the saving process, removing try-catch, and directly checking the result for success.

* refactor: add error handling back to SearchManager Chroma calls

- Wrap queryChroma calls in try-catch to prevent generator crashes
- Log Chroma errors as warnings and fall back gracefully
- Fixes generator failures when Chroma has issues
- Part of anti-pattern cleanup recovery

* feat: Add generator failure investigation report and observation duplication regression report

- Created a comprehensive investigation report detailing the root cause of generator failures during anti-pattern cleanup, including the impact, investigation process, and implemented fixes.
- Documented the critical regression causing observation duplication due to race conditions in the SDK agent, outlining symptoms, root cause analysis, and proposed fixes.

* fix: address PR #528 review comments - atomic cleanup and detector improvements

This commit addresses critical review feedback from PR #528:

## 1. Atomic Message Cleanup (Fix Race Condition)

**Problem**: SessionRoutes.ts generator error handler had race condition
- Queried messages then marked failed in loop
- If crash during loop → partial marking → inconsistent state

**Solution**:
- Added `markSessionMessagesFailed()` to PendingMessageStore.ts
- Single atomic UPDATE statement replaces loop
- Follows existing pattern from `resetProcessingToPending()`

**Files**:
- src/services/sqlite/PendingMessageStore.ts (new method)
- src/services/worker/http/routes/SessionRoutes.ts (use new method)

## 2. Anti-Pattern Detector Improvements

**Problem**: Detector didn't recognize logger.failure() method
- Lines 212 & 335 already included "failure"
- Lines 112-113 (PARTIAL_ERROR_LOGGING detection) did not

**Solution**: Updated regex patterns to include "failure" for consistency

**Files**:
- scripts/anti-pattern-test/detect-error-handling-antipatterns.ts

## 3. Documentation

**PR Comment**: Added clarification on memory_session_id fix location
- Points to SessionStore.ts:1155
- Explains why NULL initialization prevents message injection bug

## Review Response

Addresses "Must Address Before Merge" items from review:
✅ Clarified memory_session_id bug fix location (via PR comment)
✅ Made generator error handler message cleanup atomic
❌ Deferred comprehensive test suite to follow-up PR (keeps PR focused)

## Testing

- Build passes with no errors
- Anti-pattern detector runs successfully
- Atomic cleanup follows proven pattern from existing methods

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* fix: FOREIGN KEY constraint and missing failed_at_epoch column

Two critical bugs fixed:

1. Missing failed_at_epoch column in pending_messages table
   - Added migration 20 to create the column
   - Fixes error when trying to mark messages as failed

2. FOREIGN KEY constraint failed when storing observations
   - All three agents (SDK, Gemini, OpenRouter) were passing
     session.contentSessionId instead of session.memorySessionId
   - storeObservationsAndMarkComplete expects memorySessionId
   - Added null check and clear error message

However, observations still not saving - see investigation report.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* Refactor hook input parsing to improve error handling

- Added a nested try-catch block in new-hook.ts, save-hook.ts, and summary-hook.ts to handle JSON parsing errors more gracefully.
- Replaced direct error throwing with logging of the error details using logger.error.
- Ensured that the process exits cleanly after handling input in all three hooks.

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

src/servers/mcp-server.ts

@@ -73,12 +73,12 @@ async function callWorkerAPI(
 
     // Worker returns { content: [...] } format directly
     return data;
-  } catch (error: any) {
-    logger.error('SYSTEM', '← Worker API error', undefined, { endpoint, error: error.message });
+  } catch (error) {
+    logger.error('SYSTEM', '← Worker API error', { endpoint }, error as Error);
     return {
       content: [{
         type: 'text' as const,
-        text: `Error calling Worker API: ${error.message}`
+        text: `Error calling Worker API: ${error instanceof Error ? error.message : String(error)}`
       }],
       isError: true
     };
@@ -120,12 +120,12 @@ async function callWorkerAPIPost(
         text: JSON.stringify(data, null, 2)
       }]
     };
-  } catch (error: any) {
-    logger.error('HTTP', 'Worker API error (POST)', undefined, { endpoint, error: error.message });
+  } catch (error) {
+    logger.error('HTTP', 'Worker API error (POST)', { endpoint }, error as Error);
     return {
       content: [{
         type: 'text' as const,
-        text: `Error calling Worker API: ${error.message}`
+        text: `Error calling Worker API: ${error instanceof Error ? error.message : String(error)}`
       }],
       isError: true
     };
@@ -141,7 +141,7 @@ async function verifyWorkerConnection(): Promise<boolean> {
     return response.ok;
   } catch (error) {
     // Expected during worker startup or if worker is down
-    logger.debug('SYSTEM', 'Worker health check failed', undefined, { error: error instanceof Error ? error.message : String(error) });
+    logger.debug('SYSTEM', 'Worker health check failed', {}, error as Error);
     return false;
   }
 }
@@ -266,12 +266,12 @@ server.setRequestHandler(CallToolRequestSchema, async (request) => {
 
   try {
     return await tool.handler(request.params.arguments || {});
-  } catch (error: any) {
-    logger.error('SYSTEM', 'Tool execution failed', undefined, { tool: request.params.name, error: error.message });
+  } catch (error) {
+    logger.error('SYSTEM', 'Tool execution failed', { tool: request.params.name }, error as Error);
     return {
       content: [{
         type: 'text' as const,
-        text: `Tool execution failed: ${error.message}`
+        text: `Tool execution failed: ${error instanceof Error ? error.message : String(error)}`
       }],
       isError: true
     };