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/services/sync/ChromaSync.ts

@@ -283,11 +283,41 @@ export class ChromaSync {
           metadatas: cleanMetadatas
         });
       } catch (error) {
-        logger.error('CHROMA_SYNC', 'Batch add failed, continuing with remaining batches', {
-          collection: this.collectionName,
-          batchStart: i,
-          batchSize: batch.length
-        }, error as Error);
+        const errMsg = error instanceof Error ? error.message : String(error);
+        // APPROVED OVERRIDE: Duplicate IDs from partial write before timeout/crash.
+        // chroma_update_documents only updates *existing* IDs — it silently ignores
+        // missing ones. So we delete-then-add to guarantee all IDs are written.
+        if (errMsg.includes('already exist')) {
+          try {
+            await chromaMcp.callTool('chroma_delete_documents', {
+              collection_name: this.collectionName,
+              ids: batch.map(d => d.id)
+            });
+            await chromaMcp.callTool('chroma_add_documents', {
+              collection_name: this.collectionName,
+              ids: batch.map(d => d.id),
+              documents: batch.map(d => d.document),
+              metadatas: cleanMetadatas
+            });
+            logger.info('CHROMA_SYNC', 'Batch reconciled via delete+add after duplicate conflict', {
+              collection: this.collectionName,
+              batchStart: i,
+              batchSize: batch.length
+            });
+          } catch (reconcileError) {
+            logger.error('CHROMA_SYNC', 'Batch reconcile (delete+add) failed', {
+              collection: this.collectionName,
+              batchStart: i,
+              batchSize: batch.length
+            }, reconcileError as Error);
+          }
+        } else {
+          logger.error('CHROMA_SYNC', 'Batch add failed, continuing with remaining batches', {
+            collection: this.collectionName,
+            batchStart: i,
+            batchSize: batch.length
+          }, error as Error);
+        }
       }
     }