[BUG] Claude consistently ignores being directed to store plan files in the repo

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?

Despite having specified in CLAUDE.md that Claude should keep plan files in the repo until completion, it continuously ignores this.

What Should Happen?

It should allow us to persist plan files in our repo, in a plans folder. This helps keep context with the repo for plans that take a long time to complete.

Error Messages/Logs

Steps to Reproduce

Tell claude to update its claude.md that plans should be persisted in a plans folder in the repo.
Then ask it to make a plan in plan mode. The plan will not arrive in the plan folder, instead defaulting to the user home directory.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.42

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

Using latest vscode plugin as well.