[BUG] Duplicate project entries shown in project dropdown

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?

The Claude Code app shows two separate project entries for the same repository in the project dropdown:

CardAudit RayCxggg (labeled by GitHub remote owner)
CardAudit ~/Projects (labeled by local path)
Both point to the same underlying project. One of them has no sessions and appears empty.

What Should Happen?

A single project entry should appear for a given repository/directory.

Error Messages/Logs

Steps to Reproduce

1. Clone a GitHub repo (e.g., RayCxggg/CardAudit) into a local directory (e.g., ~/Projects/CardAudit)
2. Use Claude Code in that directory across multiple sessions (including some that created git worktrees)
3. Open the project dropdown in the Claude Code app
4. Two entries appear for the same repo — one identified by GitHub owner, one by local path

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.87

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Your Claude Code app version is 2.1.87.