[Bug]: Sync Config destroys .mcp.json

[slazarov]

Describe the bug

App does not load .mcp.json. Sync Config destroys .mcp.json. Leaves only:

{
"mcpServers": {}
}

Steps to reproduce

1. Open a project.
2. .mcp.json is not loaded
3. Click Sync Config
4. Empties the existing .mcp.json

Expected behavior

Loads the project's .mcp.json

Screenshots

No response

Operating System

macOS (Apple Silicon)

App Version

3.8.0

Debug logs

[2026-04-11 13:12:03.529] [INFO] [debug] App version: 3.8.0
[2026-04-11 13:12:03.529] [INFO] [debug] Platform: macos
[2026-04-11 13:12:03.529] [INFO] [debug] Debug mode restored from persisted state
[2026-04-11 13:12:04.016] [INFO] [frontend] [Debug] App started with debug mode enabled
[2026-04-11 13:12:04.055] [INFO] [frontend] [spinnerVerbLibrary] Loading spinner verbs...
[2026-04-11 13:12:04.057] [INFO] [frontend] [spinnerVerbLibrary] Loaded 0 verbs, mode=append
[2026-04-11 13:12:05.260] [INFO] [frontend] [sessionStore] Loaded 11 projects
[2026-04-11 13:12:12.644] [INFO] [frontend] [claudeSettingsLibrary] Loading settings...
[2026-04-11 13:12:12.645] [INFO] [frontend] [claudeSettingsLibrary] Loaded settings
[2026-04-11 13:12:12.668] [INFO] [frontend] [hookLibrary] Getting hooks for project id=16
[2026-04-11 13:12:32.738] [INFO] [frontend] [projectsStore] Syncing config for project id=16
[2026-04-11 13:12:32.747] [INFO] [frontend] [projectsStore] Synced config for project id=16
[2026-04-11 13:12:46.881] [INFO] [frontend] [projectsStore] Loading projects...
[2026-04-11 13:12:46.886] [INFO] [frontend] [projectsStore] Loaded 29 projects
[2026-04-11 13:12:46.886] [INFO] [frontend] [claudeSettingsLibrary] Loading settings...
[2026-04-11 13:12:46.889] [INFO] [frontend] [claudeSettingsLibrary] Loaded settings

Additional context

No response

Checklist

• I have searched existing issues to ensure this bug hasn't been reported
• I am using the latest version of the app
• I have attached debug logs (Settings > Global Settings > Debug Mode)

[slazarov]

Hello, tried 3.8.3. Same thing happens.

1. Manually create .mcp.json with config.
2. Sync
3. Empties the existing .mcp.json.

Creates an .mcp.json.bak though.

[tylergraydev]

Thanks for retesting on 3.8.3 @slazarov — confirmed this is still an issue.

Root cause: write_project_config in config_writer.rs unconditionally replaces the mcpServers key with whatever the database returns. If the project has no MCP assignments in the app's DB (e.g. servers were configured directly in .mcp.json), it overwrites with {"mcpServers": {}}.

Fix: The sync now skips overwriting mcpServers when the DB has no servers, so externally-managed .mcp.json files are preserved. The same fix was applied to write_global_config as well.

Will be in the next release.

[tylergraydev]

This is fixed in v3.8.3 (https://github.com/tylergraydev/claude-code-tool-manager/releases/tag/v3.8.3).

Specifically:

• b01f1b1 — the direct fix for Sync Config overwriting .mcp.json (PR [Bug]: Sync Config destroys .mcp.json #191).
• 5e08f89 — additional hardening: backup protection on all user file writes, so even if a writer bug sneaks in, the previous contents are preserved as .bak.

You were reporting against 3.8.0 — please update to 3.8.3 and the issue should be resolved. If you still see it happening on 3.8.3, reopen with fresh debug logs and we'll dig in.

Thanks for the report!

[slazarov]

Hello @tylergraydev . This is against 3.8.4 (tested with brew and dmg). The same behaviour again. The project appears empty apart from added hooks, i.e no skills, commands, mcps or commands. Syncing the config overwrites .mcp.json and opencode.json with empty settings and backups the existing files.

You can also see that open_folder and update_project_editor_type are missing.

[2026-04-21 06:47:12.515] [INFO] [debug] Debug logging enabled
[2026-04-21 06:47:12.515] [INFO] [debug] Log file: /Users/slazarov/Library/Application Support/com.claude-code-tool-manager.app/logs/debug-2026-04-21-064712.log
[2026-04-21 06:47:12.515] [INFO] [debug] App version: 3.8.4
[2026-04-21 06:47:12.515] [INFO] [debug] Platform: macos
[2026-04-21 06:47:29.995] [INFO] [frontend] [claudeSettingsLibrary] Loading settings...
[2026-04-21 06:47:29.996] [INFO] [frontend] [claudeSettingsLibrary] Loaded settings
[2026-04-21 06:47:30.005] [INFO] [frontend] [hookLibrary] Getting hooks for project id=30
[2026-04-21 06:47:33.292] [ERROR] [frontend] Command open_folder not found
[2026-04-21 06:47:36.633] [INFO] [frontend] [projectsStore] Syncing config for project id=30
[2026-04-21 06:47:36.637] [INFO] [frontend] [projectsStore] Synced config for project id=30
[2026-04-21 06:48:10.255] [INFO] [frontend] [claudeSettingsLibrary] Loading settings...
[2026-04-21 06:48:10.256] [INFO] [frontend] [claudeSettingsLibrary] Loaded settings
[2026-04-21 06:48:10.266] [INFO] [frontend] [hookLibrary] Getting hooks for project id=30
[2026-04-21 06:48:13.052] [ERROR] [frontend] Command update_project_editor_type not found