[Bug] Permissions configuration files not persisting across sessions

Bug Description
The permissions document on my machine is not working despite exentsive troubleshooting. settings.json and setting.local.json are not acknowledged by claude code - for example, none of my allows are saved correctly, and no denies or asks I enter are either. Every session ends up asking for permissions for everything all the time. I have tried manually adding allows and denies into these files, but upon startup and running, claude code rewrites the file anew no matter what is in it. I have verified this in both the master .claude folder and at subdirectories where i am executing my work. Claude has worked with me to tackle this issue and has concluding i should submit a bug.

Environment Info

• Platform: darwin
• Terminal: Apple_Terminal
• Version: 2.0.59
• Feedback ID:

Errors

[{"error":"U01: Insufficient permissions for global npm install.\n    at Oo1 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1454:986)\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)\n    at async nNA (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1464:43)\n    at async file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:2692:9769","timestamp":"2026-01-27T02:04:23.242Z"},{"error":"U01: Insufficient permissions for global npm install.\n    at Oo1 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1454:986)\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)\n    at async nNA (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:1464:43)\n    at async file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:2692:9769","timestamp":"2026-01-27T02:04:37.706Z"},{"error":"AxiosError: Request failed with status code 403\n    at VS (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:171:1137)\n    at IncomingMessage.<anonymous> (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:172:9854)\n    at IncomingMessage.emit (node:events:531:35)\n    at IncomingMessage.emit (node:domain:488:12)\n    at endReadableNT (node:internal/streams/readable:1696:12)\n    at process.processTicksAndRejections (node:internal/process/task_queues:82:21)\n    at YDA.request (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:174:2130)\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)\n    at async UD0 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:4467:3928)","timestamp":"2026-01-27T02:04:38.541Z"},{"error":"AxiosError: Request failed with status code 403\n    at VS (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:171:1137)\n    at IncomingMessage.<anonymous> (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:172:9854)\n    at IncomingMessage.emit (node:events:531:35)\n    at IncomingMessage.emit (node:domain:488:12)\n    at endReadableNT (node:internal/streams/readable:1696:12)\n    at process.processTicksAndRejections (node:internal/process/task_queues:82:21)\n    at YDA.request (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:174:2130)\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)\n    at async UD0 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:4467:3928)","timestamp":"2026-01-27T02:05:00.749Z"},{"error":"AxiosError: Request failed with status code 403\n    at VS (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:171:1137)\n    at IncomingMessage.<anonymous> (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:172:9854)\n    at IncomingMessage.emit (node:events:531:35)\n    at IncomingMessage.emit (node:domain:488:12)\n    at endReadableNT (node:internal/streams/readable:1696:12)\n    at process.processTicksAndRejections (node:internal/process/task_queues:82:21)\n    at YDA.request (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:174:2130)\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)\n    at async UD0 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:4467:3928)","timestamp":"2026-01-27T02:05:18.953Z"},{"error":"AxiosError: Request failed with status code 403\n    at VS (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:171:1137)\n    at IncomingMessage.<anonymous> (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:172:9854)\n    at IncomingMessage.emit (node:events:531:35)\n    at IncomingMessage.emit (node:domain:488:12)\n    at endReadableNT (node:internal/streams/readable:1696:12)\n    at process.processTicksAndRejections (node:internal/process/task_queues:82:21)\n    at YDA.request (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:174:2130)\n    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)\n    at async UD0 (file:///usr/local/lib/node_modules/@anthropic-ai/claude-code/cli.js:4

Note: Error logs were truncated.