Git commit permission prompt appears repeatedly despite allow tools configuration

Issue Description

Git commit permission prompt appears every time despite properly configuring git commit in BOTH global and project-local settings files.

Steps to Reproduce

1. Configure git commit in both global and project settings files
2. Attempt to commit changes using git commit
3. Permission prompt appears every time despite the configuration

Expected Behavior

Permission prompt should not appear when git commit is listed in permissions.allow.

Actual Behavior

Permission prompt appears repeatedly for every git commit operation, ignoring both global and project-local settings.

Environment

• Platform: macOS
• OS Version: Darwin 24.5.0
• Date observed: 2025/5/31
• Claude Code model: claude-opus-4-20250514

Current Configuration

claude config list output:

{
  "allowedTools": [],
  "dontCrawlDirectory": false,
  "hasTrustDialogAccepted": true,
  "hasCompletedProjectOnboarding": true
}

Global settings (~/.claude/settings.json):

{
  "permissions": {
    "allow": [
      "Bash(git for-each-ref:*)",
      "Bash(git branch:*)", 
      "Bash(rg:*)",
      "Bash(grep:*)",
      "Bash(pnpm run check:*)",
      "Bash(git add:*)",
      "Bash(git push:*)",
      "Bash(pnpm test:*)",
      "Bash(npx vitest:*)",
      "Bash(find:*)",
      "Bash(pnpm run test:unit:*)",
      "Bash(rm:*)",
      "Bash(mv:*)",
      "Bash(git commit:*)",
      "Bash(git checkout:*)",
      "Bash(gh pr create:*)",
      "Bash(git fetch:*)",
      "Bash(git reset:*)",
      "Bash(pnpm install:*)",
      "Bash(cat:*)",
      "Bash(curl:*)"
    ],
    "deny": []
  },
  "model": "opus"
}

Project-local settings (.claude/settings.local.json):

{
  "permissions": {
    "allow": [
      "Bash(git for-each-ref:*)",
      "Bash(git branch:*)",
      "Bash(rg:*)",
      "Bash(grep:*)",
      "Bash(pnpm run check:*)",
      "Bash(git add:*)",
      "Bash(git push:*)",
      "Bash(pnpm test:*)",
      "Bash(npx vitest:*)",
      "Bash(find:*)",
      "Bash(pnpm run test:unit:*)",
      "Bash(rm:*)",
      "Bash(mv:*)",
      "Bash(git commit:*)",
      "Bash(git checkout:*)",
      "Bash(gh pr create:*)",
      "Bash(git fetch:*)",
      "Bash(git reset:*)",
      "Bash(pnpm install:*)"
    ],
    "deny": []
  },
  "enableAllProjectMcpServers": false
}

Additional Context

• Git commit is explicitly listed in BOTH global and project-local settings files as "Bash(git commit:*)"
• Other git commands (like add, push, checkout) work without permission prompts
• The legacy claude config add allowedTools shows a deprecation warning, confirming settings.json is the correct method
• Settings are being read correctly as other allowed commands work without prompts
• This appears to be a bug specific to git commit command permissions

Steps to Verify

1. Both configuration files exist and contain valid JSON
2. Both files explicitly include "Bash(git commit:*)" in permissions.allow
3. Other git commands in the same allow lists work correctly
4. Only git commit triggers permission prompts despite proper configuration