[BUG] Claude Code ignoring VCS workflow instructions telling it to use jj

Environment

• Platform (select one):
• [x ] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.56
• Operating System: Fedora Workstation 42-1.1

Bug Description

claude was given clear instructions to use jj in the project's CLAUDE.md file:

## VCS workflow

It is *CRITICAL* that you follow this section.

This project uses `jj` as its VCS.  `jj` docs can be found in the docs folder of the `jj-vcs/jj` repository on [Github](https://github.com/jj-vcs/jj/).

We follow the Squash Workflow as described [here](https://steveklabnik.github.io/jujutsu-tutorial/real-world-workflows/the-squash-workflow.html).  In practice this means that at the start of any new conversation which may involve changes to project files you *MUST*:

1. create a new, empty change and include a short description via the `-m` flag, i.e. `jj new -m $message`. You *MUST* prefix your descriptions with 'CLAUDE:' so that I know it was you.
2. to work on an item on your `TO-DO` list create a new empty change on top of that one, i.e. `jj new`
3. only after you have tested and verified that your change works, you use `jj squash` to move the changes from `@` into the change where you described the overall task.

You must *NEVER* use `jj squash`to move your changes into a parent revision that you did not create, i.e. do not tamper with history.

Conversation history was cleared with /clear and claude was explicitly told to re-read CLAUDE.md with the prompt re-read CLAUDE.md. Claude acknowledged the need to use jj in its output "... with strict development guidelines including: - Use of jj VCS with Squash Workflow".

But when asked to do a simple task, e.g. "update the dependency information in the README file" it proceeded to immediately edit the README file. Claude DID NOT run jj new before starting, and Claude did not run any jj commands after finishing. Claude made ZERO effort to use jj, let alone making any effort to use the specified jj workflow.