Method freshen

src/mcp/tools.ts:1117–1130

* Heal a long-lived connection whose `.codegraph/` was removed and recreated * at the same path (a worktree recreated, or `rm -rf .codegraph` + re-init) * before handing it to a tool. Otherwise the daemon keeps serving the * pre-removal snapshot from its now-unlinked file handle until resta

(cg: CodeGraph)

   * tool call.
   */
  private freshen(cg: CodeGraph): CodeGraph {
    try {
      if (cg.reopenIfReplaced()) {
        process.stderr.write(
          '[CodeGraph MCP] The index was replaced on disk (e.g. a git worktree ' +
          'recreated at the same path); reopened the live database in place.\n'
        );
      }
    } catch {
      // Best-effort self-heal — a failed reopen must never break the tool call;
      // the (still stale) handle keeps serving and the next call retries.
    }
    return cg;
  }

  /**
   * Close all cached project connections