[BUG] Workspace Trust Dialog Not Respecting Pre-configured ~/.claude/.claude.json

[matguthrie]

Preflight Checklist

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

What's Wrong?

Workspace trust dialogs appear every time Claude Code is launched in a git worktree subdirectory, even when the worktree path has been pre-configured in ~/.claude/.claude.json with allowedTools: []. This blocks automated multi-agent orchestration workflows where Claude instances are spawned
programmatically in isolated worktrees.

The ~/.claude/.claude.json configuration correctly contains the worktree path:
{
"projects": {
"/workspace/worktrees/initialize-blazor-server-project-task-qnh0ys8fs": {
"allowedTools": []
}
}
}

However, when spawning Claude in this exact path, the "Do you trust the files in this folder?" dialog still appears, requiring manual approval despite the pre-configuration.

What Should Happen?

When a workspace path is pre-configured in ~/.claude/.claude.json under the projects object with allowedTools: [], Claude Code should recognize this as a trusted workspace and skip the workspace trust dialog on launch.

This would enable:

• Automated spawning of Claude instances in worktrees without manual intervention
• Multi-agent orchestration systems where multiple Claude instances work in parallel
• CI/CD integration where Claude processes run in subdirectories

Error Messages/Logs

Steps to Reproduce

1. Create a git worktree subdirectory:
   git worktree add /workspace/worktrees/test-task-123 -b test-branch
2. Pre-configure workspace trust in ~/.claude/.claude.json:
   cat > ~/.claude/.claude.json << 'EOF'
   {
   "projects": {
   "/workspace/worktrees/test-task-123": {
   "allowedTools": []
   }
   }
   }
   EOF
3. Launch Claude Code in the worktree with permission bypass flags:
   cd /workspace/worktrees/test-task-123
   claude --dangerously-skip-permissions --permission-mode bypassPermissions
4. Expected: Claude launches without prompts
   Actual: "Do you trust the files in this folder?" dialog appears

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.0.8

Claude Code Version

2.0.10

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

Environment:

• Claude Code Version: 2.0.9+
• Platform: Linux (WSL2 in Docker devcontainer)
• Terminal: tmux
• Parent directory: Git repository with worktrees
• Worktree structure: /workspace/worktrees/{task-id}/

Workaround:
Manually clicking "Yes, proceed" on first launch per worktree, but this defeats automated workflows.

Feature Request:
Add a command-line flag like --trusted-workspace or --skip-trust-dialog for automation use cases where the workspace is known to be safe.

[normalnormie]

v2.0.8
[...] Remove deprecated .claude.json allowedTools, ignorePatterns, env, and todoFeatureEnabled config options (instead, configure these in your settings.json)
Oct 5, 2025

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[github-actions]

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