[BUG] Project specific memory to can be stored in the wrong project.

### Preflight Checklist

- [x] I have searched [existing issues](https://github.com/anthropics/claude-code/issues?q=is%3Aissue%20state%3Aopen%20label%3Abug) 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?

Project specific memory to can be stored in the wrong project.

### What Should Happen?

EXPECTED: Project specific memory to be stored with the project.

### Error Messages/Logs

```shell
N/A
```

### Steps to Reproduce

1) Fresh install, new account. Go to Claude Code
2) Open a local repo folder. Do work (or not. does not affect bug)
3) Open a different repo/project. Do work.
RESULT: Recent project specific memory is stored in the first repo opened.
EXPECTED: Project specific memory to be stored with the project.

### Claude Model

Sonnet (default)

### Is this a regression?

I don't know

### Last Working Version

N/A

### Claude Code Version

Unknown command: /claude

### Platform

Anthropic API

### Operating System

Windows

### Terminal/Shell

Terminal.app (macOS)

### Additional Information

It is also extremely hard to switch projects... But that's a different bug... No way to make a new thread with a different repo.

No source file or test is identified in the report. Start by reproducing the behavior across two local repository folders in Claude Code, then trace how project-specific memory is selected and stored when switching projects. Done means recent project memory remains associated with the project where it was created.

Written by the indexing model from the issue text.