private async indexFile(
  entry: MemoryFileEntry | SessionFileEntry,
  options: { source: MemorySource; content?: string },
) {
  // ... embedding logic ...

  // DELETE operations without transaction
  if (vectorReady) {
    try {
      this.db
        .prepare(
          `DELETE FROM ${VECTOR_TABLE} WHERE id IN (SELECT id FROM chunks WHERE path = ? AND source = ?)`,
        )
        .run(entry.path, options.source);
    } catch {}
  }
  if (this.fts.enabled && this.fts.available) {
    try {
      this.db
        .prepare(`DELETE FROM ${FTS_TABLE} WHERE path = ? AND source = ? AND model = ?`)
        .run(entry.path, options.source, this.provider.model);
    } catch {}
  }
  this.db
    .prepare(`DELETE FROM chunks WHERE path = ? AND source = ?`)
    .run(entry.path, options.source);

  // INSERT operations in loop without transaction
  for (let i = 0; i < chunks.length; i++) {
    // INSERT into chunks, VECTOR_TABLE, FTS_TABLE
  }

  // Final INSERT into files
  this.db.prepare(`INSERT INTO files ...`).run(...);
}

// Inside syncMemoryFiles method - stale entry cleanup
for (const stale of staleRows) {
  if (activePaths.has(stale.path)) continue;
  this.db.prepare(`DELETE FROM files WHERE path = ? AND source = ?`).run(stale.path, "memory");
  try {
    this.db.prepare(`DELETE FROM ${VECTOR_TABLE} WHERE id IN ...`).run(stale.path, "memory");
  } catch {}
  this.db.prepare(`DELETE FROM chunks WHERE path = ? AND source = ?`).run(stale.path, "memory");
  if (this.fts.enabled && this.fts.available) {
    try {
      this.db.prepare(`DELETE FROM ${FTS_TABLE} WHERE path = ? AND source = ? AND model = ?`).run(...);
    } catch {}
  }
}

for (const stale of staleRows) {
  if (activePaths.has(stale.path)) continue;
  params.db.prepare(`DELETE FROM files WHERE path = ? AND source = ?`).run(stale.path, "memory");
  try {
    params.db.prepare(`DELETE FROM ${params.vectorTable} WHERE id IN ...`).run(stale.path, "memory");
  } catch {}
  params.db.prepare(`DELETE FROM chunks WHERE path = ? AND source = ?`).run(stale.path, "memory");
  if (params.ftsEnabled && params.ftsAvailable) {
    try {
      params.db.prepare(`DELETE FROM ${params.ftsTable} WHERE path = ? AND source = ? AND model = ?`).run(...);
    } catch {}
  }
}

for (const stale of staleRows) {
  if (activePaths.has(stale.path)) continue;
  params.db.prepare(`DELETE FROM files WHERE path = ? AND source = ?`).run(stale.path, "sessions");
  try {
    params.db.prepare(`DELETE FROM ${params.vectorTable} WHERE id IN ...`).run(stale.path, "sessions");
  } catch {}
  params.db.prepare(`DELETE FROM chunks WHERE path = ? AND source = ?`).run(stale.path, "sessions");
  if (params.ftsEnabled && params.ftsAvailable) {
    try {
      params.db.prepare(`DELETE FROM ${params.ftsTable} WHERE path = ? AND source = ? AND model = ?`).run(...);
    } catch {}
  }
}

// Example for indexFile method
private async indexFile(
  entry: MemoryFileEntry | SessionFileEntry,
  options: { source: MemorySource; content?: string },
) {
  // ... embedding logic unchanged ...

  const now = Date.now();

  try {
    this.db.exec("BEGIN");

    // All DELETE operations
    if (vectorReady) {
      try {
        this.db.prepare(`DELETE FROM ${VECTOR_TABLE} WHERE id IN ...`).run(...);
      } catch {}
    }
    // ... other deletes ...

    // All INSERT operations in loop
    for (let i = 0; i < chunks.length; i++) {
      // ... inserts ...
    }

    // Final files INSERT
    this.db.prepare(`INSERT INTO files ...`).run(...);

    this.db.exec("COMMIT");
  } catch (err) {
    try {
      this.db.exec("ROLLBACK");
    } catch {}
    throw err;
  }
}