[BUG] Claude Code treats bind mounts and symlinks as separate projects in .claude.json

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 the same directory is accessible via multiple paths (bind mounts, symlinks, or multiple NFS mounts), each path is treated as a separate project with independent settings, trust dialogs, and onboarding states.

For example,
/home/user is the symlink of /nfs/home/user. However, I have two entries in config that are mismatched. And modification to one doesn't reflect to the other.

"/home/user": {
"allowedTools": [],
"hasTrustDialogAccepted": false,
"projectOnboardingSeenCount": 4,
"lastSessionId": "7739c417-838e-4726-866b-2ba46c56873a"
},
"/nfs/home/user": {
"allowedTools": [],
"hasTrustDialogAccepted": true,
"projectOnboardingSeenCount": 0,
"lastSessionId": "04d8aaae-76c6-499c-923f-53ab0b1b03e5"
},

Everytime i open Claude from /home/user, it keeps showing the
Do you trust the files in this folder?
/home/user

❯ 1. Yes, proceed

What Should Happen?

When I open Claude the next time from /home/user, it should not show TrustDialog accepted.

Error Messages/Logs

Steps to Reproduce

1. Mount or symlink the same directory at two paths (e.g., /home/user and /nfs/home/user)
2. Run claude from /home/user
3. Run claude from /nfs/home/user
4. Check ~/.claude.json - you'll see duplicate project entries with different settings

Claude Model

None

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.6

Platform

Google Vertex AI

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_