claude-code - 💡(How to fix) Fix [Bug] Local directory permissions get copied into global settings.json on config update [2 comments, 2 participants]

[{"error":"Error: NON-FATAL: Lock acquisition failed for /home/jshute/.local/share/claude/versions/2.1.101 (expected in multi-process scenarios)\n at qQ$ (/$bunfs/root/src/entrypoints/cli.js:2838:2153)\n at Ee8 (/$bunfs/root/src/entrypoints/cli.js:2838:1233)\n at processTicksAndRejections (native:7:39)","timestamp":"2026-04-11T15:07:22.317Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n at dDH (/$bunfs/root/src/entrypoints/cli.js:1558:33935)\n at processTicksAndRejections (native:7:39)","timestamp":"2026-04-11T15:07:22.356Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n at dDH (/$bunfs/root/src/entrypoints/cli.js:1558:33935)\n at async W (/$bunfs/root/src/entrypoints/cli.js:6005:10596)\n at processTicksAndRejections (native:7:39)","timestamp":"2026-04-11T15:07:23.026Z"},{"error":"Error: Plugin MCP server error - mcp-config-invalid: MCP server github invalid: Missing environment variables: GITHUB_PERSONAL_ACCESS_TOKEN\n at dDH (/$bunfs/root/src/entrypoints/cli.js:1558:33935)\n at async v (/$bunfs/root/src/entrypoints/cli.js:6005:11366)\n at processTicksAndRejections (native:7:39)","timestamp":"2026-04-11T15:07:23.028Z"}]

TL;DR

The issue can be mitigated by modifying the code to prevent merging local permissions into global settings when updating the /config endpoint.

Guidance

• Review the code in cli.js around lines 2838 and 1558 to understand how permissions are being merged and how errors are being handled.
• Verify that the settings.local.json and settings.json files are being read and written correctly, and that the defaultMode setting is being updated as expected.
• Consider adding a check to prevent the merging of local permissions into global settings when the /config endpoint is updated.
• Investigate the missing GITHUB_PERSONAL_ACCESS_TOKEN environment variable and its impact on the MCP server error.

Example

No code snippet can be provided without modifying the existing codebase, but the fix likely involves modifying the cli.js file to handle permissions merging correctly.

Notes

The provided error messages indicate issues with lock acquisition and missing environment variables, but these may not be directly related to the permissions merging issue. The fix should focus on preventing the unwanted merging of local permissions into global settings.

Recommendation

Apply a workaround by modifying the code to prevent merging local permissions into global settings when updating the /config endpoint, as the root cause of the issue appears to be related to the handling of permissions in the cli.js file.