[BUG] Permanent permission approval overwrites entire allow array instead of appending

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?

When selecting option 2 "Allow permanently" for a permission request, Claude
Code overwrites the entire allow array in .claude/settings.local.json instead of appending the new permission to the existing array.

All previous permissions are deleted.

What Should Happen?

The new permission should be appended to the existing array:
``{
"permissions": {
"allow": [
"Read",
"Glob",
"Grep",
...
"Bash(npx biome migrate*)"
]
}
}``

Error Messages/Logs

Steps to Reproduce

1. Have existing permissions in .claude/settings.local.json:

```json
{
"permissions": {
"allow": [
"Read",
"Glob",
"Grep",
"Bash(npm run test:*)",
"Bash(npm run lint:*)",
"Bash(npm run lint:biome:*)",
"Bash(npm run format:*)",
"Bash(npm run format:biome:*)",
"Bash(npm run build)",
"Bash(npm run typecheck:*)",
"Bash(npm run typegen:*)",
"Bash(git status)",
"Bash(git log*)",
"Bash(git diff*)",
"Bash(git branch*)",
"Bash(git remote*)",
"Bash(git ls-files*)",
"Bash(git blame*)",
"Bash(ls*)",
"Bash(cat*)",
"Bash(head*)",
"Bash(tail*)",
"Bash(pwd)",
"Bash(tree*)",
"Bash(du*)",
"Bash(wc*)",
"Bash(file*)",
"BashOutput",
"Bash(curl*)",
"Bash(wget*)",
"Bash(ping*)",
"Bash(npm install*)",
"Bash(npm list*)",
...
]
}
}

1. Claude requests a new permission (e.g., npx biome migrate)
2. Select option 2 "Allow permanently"
3. Check .claude/settings.local.json

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.37 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_