Method sync

src/extraction/index.ts:1938–2074

* Sync the index with the current file state. * * Change detection is filesystem-based, never git: a (size, mtime) stat * pre-filter skips unchanged files, then a content-hash compare confirms real * changes. This works in non-git projects and catches committed changes from * `git pul

(onProgress?: (progress: IndexProgress) => void)

   * `git pull`/`checkout`/`merge`/`rebase` that `git status` cannot see.
   */
  async sync(onProgress?: (progress: IndexProgress) => void): Promise<SyncResult> {
    await initGrammars(); // Initialize WASM runtime (grammars loaded lazily below)
    const startTime = Date.now();
    let filesChecked = 0;
    let filesAdded = 0;
    let filesModified = 0;
    let filesRemoved = 0;
    let nodesUpdated = 0;
    const changedFilePaths: string[] = [];

    onProgress?.({
      phase: 'scanning',
      current: 0,
      total: 0,
    });

    const filesToIndex: string[] = [];
    // === Filesystem reconcile (git-independent) ===
    // The source of truth for "what changed" is the filesystem vs the indexed
    // state — never git. We enumerate the current source files and reconcile
    // each against the DB. A cheap (size, mtime) stat pre-filter skips unchanged
    // files without reading or hashing them, so the expensive read+hash+parse
    // only runs for files that actually changed. This catches edits/adds/deletes
    // whether or not the project uses git, and crucially also catches committed
    // changes from `git pull`/`checkout`/`merge`/`rebase` — which `git status`
    // cannot see, because the working tree is clean afterward.
    const currentFiles = await scanDirectoryAsync(this.rootDir);
    filesChecked = currentFiles.length;
    const currentSet = new Set(currentFiles);

    const trackedFiles = this.queries.getAllFiles();
    const trackedMap = new Map<string, FileRecord>();
    for (const f of trackedFiles) {
      trackedMap.set(f.path, f);
    }

    // Removals: tracked in the DB but no longer a present source file. Check the
    // filesystem directly — `scanDirectory` (via `git ls-files`) still lists a
    // file deleted from disk but not yet staged, so set membership alone misses it.
    // `reconcileChecks` drives the cooperative yield shared with the adds/mods loop
    // below (see SYNC_RECONCILE_YIELD_INTERVAL / issue #905).
    let reconcileChecks = 0;
    for (const tracked of trackedFiles) {
      if (!currentSet.has(tracked.path) || !fs.existsSync(path.join(this.rootDir, tracked.path))) {
        this.queries.deleteFile(tracked.path);
        filesRemoved++;
      }
      if (++reconcileChecks % SYNC_RECONCILE_YIELD_INTERVAL === 0) {
        await new Promise<void>((resolve) => setImmediate(resolve));
      }
    }

    // Adds / modifications.
    for (const filePath of currentFiles) {
      // Same cooperative yield as the removals loop — this is the other O(files)
      // synchronous-stat loop that wedges the main thread on a large repo (#905).
      // Yield at the top of the body so the `continue` fast-paths below still hit it.
      if (++reconcileChecks % SYNC_RECONCILE_YIELD_INTERVAL === 0) {