[Bug] Persistent Permission Prompts Ignore Previously Granted Access

Bug Description
Asking me for permission to read/search every single folder. Seems to ignore every granted permission and needs explicit prompt always

Environment Info

• Platform: win32
• Terminal: windows-terminal
• Version: 1.0.107
• Feedback ID: ec4a576c-2395-415b-b0e1-6fc5881fb063

Errors

[{"error":"Error: Error opening file C:\\Users\\roverby\\.claude\\projects\\c--users-roverby-source-repos-mega-MedEx\\6c4ce8cd-9c0c-4d32-b638-28e946a68aae.jsonl: Error: ENOENT: no such file or directory, open 'C:\\Users\\roverby\\.claude\\projects\\c--users-roverby-source-repos-mega-MedEx\\6c4ce8cd-9c0c-4d32-b638-28e946a68aae.jsonl'\n    at Gs1 (file:///C:/Users/roverby/AppData/Local/nvm/v24.6.0/node_modules/@anthropic-ai/claude-code/cli.js:692:176)\n    at async eo1 (file:///C:/Users/roverby/AppData/Local/nvm/v24.6.0/node_modules/@anthropic-ai/claude-code/cli.js:746:1639)\n    at async file:///C:/Users/roverby/AppData/Local/nvm/v24.6.0/node_modules/@anthropic-ai/claude-code/cli.js:746:2074\n    at async fVA.appendEntry (file:///C:/Users/roverby/AppData/Local/nvm/v24.6.0/node_modules/@anthropic-ai/claude-code/cli.js:743:43)\n    at async fVA.insertMessageChain (file:///C:/Users/roverby/AppData/Local/nvm/v24.6.0/node_modules/@anthropic-ai/claude-code/cli.js:742:36772)\n    at async UD1 (file:///C:/Users/roverby/AppData/Local/nvm/v24.6.0/node_modules/@anthropic-ai/claude-code/cli.js:745:2506)","timestamp":"2025-09-05T14:44:40.343Z"}]