[BUG] Claude Code via Windows Terminal Storing Python Commands when "Allow All" is selected

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

• "Allow All" stores verbatim command text instead of extracting base commands
• Multiline commands create invalid fragment entries (do, done, fi, break)
• __NEW_LINE__ internal markers leak into stored permissions
• No validation that stored entries are valid commands
• File grows unbounded until it causes crashes/session termination
• Workaround: manually reset ~/.claude/settings.local.json

What Should Happen?

Nothing gets stored in the config file when ALLOW ALL is selected

Error Messages/Logs

- "Allow All" stores verbatim command text instead of extracting base commands
  - Multiline commands create invalid fragment entries (do, done, fi, break)
  - __NEW_LINE__ internal markers leak into stored permissions

Steps to Reproduce

Go into claude code for Win Terminal, add ALLOW ALL to commands, then log out / log in and see the error in the config file

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.76

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_