fix: resolve 3 upstream bugs (summarize, ChromaSync, HealthMonitor) (#1566)

* fix: resolve 3 upstream bugs in summarize, ChromaSync, and HealthMonitor

1. summarize.ts: Skip summary when transcript has no assistant message.
   Prevents error loop where empty transcripts cause repeated failed
   summarize attempts (~30 errors/day observed in production).

2. ChromaSync.ts: Fallback to chroma_update_documents when add fails
   with "IDs already exist". Handles partial writes after MCP timeout
   without waiting for next backfill cycle.

3. HealthMonitor.ts: Replace HTTP-based isPortInUse with atomic socket
   bind on Unix. Eliminates TOCTOU race when two sessions start
   simultaneously (HTTP check is non-atomic — both see "port free"
   before either completes listen()). Updated tests accordingly.

All three bugs are pre-existing in v10.5.5. Confirmed via log analysis
of 543K lines over 17 days of production usage across two servers.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* chore: add CONTRIB_NOTES.md to gitignore

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: address CodeRabbit review on PR #1566

- HealthMonitor: add APPROVED OVERRIDE annotation for Win32 HTTP fallback
- ChromaSync: replace chroma_update_documents with delete+add for proper
  upsert (update only modifies existing IDs, silently ignores missing ones)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Alessandro Costa <alessandro@claudio.dev>
Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

src/cli/handlers/summarize.ts

@@ -52,6 +52,16 @@ export const summarizeHandler: EventHandler = {
       return { continue: true, suppressOutput: true, exitCode: HOOK_EXIT_CODES.SUCCESS };
     }
 
+    // Skip summary if transcript has no assistant message (prevents repeated
+    // empty summarize requests that pollute logs — upstream bug)
+    if (!lastAssistantMessage || !lastAssistantMessage.trim()) {
+      logger.debug('HOOK', 'No assistant message in transcript - skipping summary', {
+        sessionId,
+        transcriptPath
+      });
+      return { continue: true, suppressOutput: true, exitCode: HOOK_EXIT_CODES.SUCCESS };
+    }
+
     logger.dataIn('HOOK', 'Stop: Requesting summary', {
       hasLastAssistantMessage: !!lastAssistantMessage
     });