Method sync

src/index.ts:777–1035

* Sync with current file state (incremental update) * * Uses a mutex to prevent concurrent indexing operations.

(options: IndexOptions = {})

   * Uses a mutex to prevent concurrent indexing operations.
   */
  async sync(options: IndexOptions = {}): Promise<SyncResult> {
    return this.indexMutex.withLock(async () => {
      try {
        this.fileLock.acquire();
      } catch {
        return { filesChecked: 0, filesAdded: 0, filesModified: 0, filesRemoved: 0, nodesUpdated: 0, durationMs: 0 };
      }
      // Defer WAL auto-checkpointing for the whole incremental run, exactly
      // as indexAll does for the bulk path (#1231): sync's store loop and its
      // resolution passes churn the same FTS + secondary-index hot pages, and
      // at the default 1000-page cadence the inline checkpoints re-write them
      // over and over — on HDD-class storage a 7-file sync took 2 minutes at
      // 0-2% CPU (#1248). The cost scales with the EXISTING database size,
      // not the change size, so small syncs on big indexes hurt most. The
      // valve bounds WAL growth off-thread; runMaintenance at the end does
      // the final fold-up before the interval is restored in the finally.
      // Same kill switch as indexAll: CODEGRAPH_NO_WAL_DEFER=1. Idle valve
      // cost is one timer, so watcher-frequency syncs stay cheap.
      const deferWal = process.env.CODEGRAPH_NO_WAL_DEFER !== '1' && this.db.getJournalMode() === 'wal';
      let walValve: WalCheckpointValve | null = null;
      let priorAutocheckpoint = 1000;
      if (deferWal) {
        priorAutocheckpoint = this.db.getWalAutocheckpoint();
        this.db.setWalAutocheckpoint(0);
        walValve = new WalCheckpointValve(
          this.db,
          resolveWalValveMb(process.env.CODEGRAPH_WAL_VALVE_MB, this.db.getDbFileSizeBytes()),
          undefined,
          options.verbose ? (m) => console.log(`[wal-valve] ${m}`) : undefined
        );
        walValve.start();
      }
      try {
        // Captured BEFORE the sync runs: the sync's own incremental writes
        // populate vocab rows for the files it touches, so an end-of-sync
        // emptiness check would see "non-empty" and skip the backfill forever,
        // leaving every unchanged file's names unsegmented.
        const vocabWasEmpty = (() => {
          try { return this.queries.isNameSegmentVocabEmpty(); } catch { return false; }
        })();

        const result = await this.orchestrator.sync(options.onProgress, options.paths);

        // Fold the store phase's WAL BEFORE the post-store reads below
        // (resolution reads on the main thread) — same rationale as
        // indexAll's fold between store and resolution.
        if (walValve) await walValve.foldNow();

        // Cross-file finalization (e.g. NestJS RouterModule prefixes). Run on
        // every sync that touched files so edits to `app.module.ts` propagate
        // to controllers in unchanged files. The pass is idempotent and cheap
        // (regex over *.module.ts only).
        if (result.filesAdded > 0 || result.filesModified > 0) {
          this.resolver.runPostExtract();
        } else if (result.filesRemoved > 0) {
          // A pure-removal sync still resolves refs below — the deletion path
          // resurrects the removed file's incoming edges as pending refs
          // (#1240 removal case) and the orphan sweep consumes them. In a