fix(sync): refresh synthesized edges after incremental changes (#1988) (#2033)

* fix(sync): refresh synthesized edges after incremental changes (#1988)

Scoped sync skipped synthesis and retained obsolete dispatch edges.
Refresh all synthesis passes after base resolution when dependencies or source patterns change.
Stage and atomically replace owned edges, preserve ordinary edges, and retry interrupted refreshes.
Stabilize traversal order and migrate existing indexes for rebuild convergence.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix: preserve structural Go containment during synthesis refresh

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

src/extraction/index.ts

@@ -3037,7 +3037,9 @@ export class ExtractionOrchestrator {
      * is stored, when no extraction transaction is open, so a checkpoint can
      * safely catch up before the next file grows the WAL further.
      */
-    backpressure?: () => Promise<void> | null
+    backpressure?: () => Promise<void> | null,
+    /** Inspect changed inputs before deletion/re-extraction cascades their edges. */
+    onFileChange?: (filePath: string, content?: string) => void
   ): Promise<SyncResult> {
     await initGrammars(); // Initialize WASM runtime (grammars loaded lazily below)
     const startTime = Date.now();
@@ -3153,6 +3155,7 @@ export class ExtractionOrchestrator {
             this.queries.insertUnresolvedRefsBatch(resurrected);
           }
         }
+        onFileChange?.(tracked.path);
         this.queries.deleteFile(tracked.path);
         filesRemoved++;
       }
@@ -3202,10 +3205,12 @@ export class ExtractionOrchestrator {
       const contentHash = hashContent(content);
 
       if (!tracked) {
+        onFileChange?.(filePath, content);
         filesToIndex.push(filePath);
         changedFilePaths.push(filePath);
         filesAdded++;
       } else if (tracked.contentHash !== contentHash) {
+        onFileChange?.(filePath, content);
         filesToIndex.push(filePath);
         changedFilePaths.push(filePath);
         filesModified++;