`codegraph index` fails with "database file is in use" when MCP server is still running

[bithy0825]

Environment

• OS: Windows 11 (Git Bash)
• Codegraph: 1.4.1

Steps to Reproduce

1. Install codegraph MCP into Claude Code: codegraph install
2. Use Claude Code normally
3. Exit Claude Code (either via /exit or by closing the window directly)
4. Try to rebuild the index: codegraph index

Expected

The index rebuilds successfully.

Actual

[ERR] Failed to index: Could not rebuild the index — the database file is in use
(EPERM, Permission denied: \\?\E:\workspace\aod\.codegraph\codegraph.db)

Additional Context

After exiting Claude Code (both /exit and closing the window), the MCP server process remains running on my machine. codegraph index continues to fail until I manually end the "Node.js JavaScript Runtime" process via Task Manager. After doing so, codegraph index succeeds.