[BUG] Claude keeps ignoring my gpg signing rules

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?

Sometime recently, claude code started to experience a ton of issues for me where I have gpg signing set up on my machine but I have in my CLAUDE.md instructions to not use it. To do a "no sign" when committing. However, it keeps ignoring that. Turns out it is because it is in conflict with the system prompt that has:

NEVER skip hooks (--no-verify) or bypass signing (--no-gpg-sign, -c commit.gpgsign=false) unless the user has explicitly asked for it.

Well, I am explicitly asking for it in my CLAUDE.md but it gets ignored a decent amount of the time now. I'd really like a way to be able to turn off system prompt items as I suspect this isnt going to be an isolated case of conflict that will arise. That said, the surface level issue here is that the system prompt keeps overriding my CLAUDE.md. The deeper concern is that you can add things to the system prompt at any time that will change my experience for the worse and that I won't be able to override them (or even know about the spooky action a distance).

What Should Happen?

Claude shouldnt ignore my system prompt overrides and I shouldn't have to worry about you introducing spooky actions at a distance.

Error Messages/Logs

n/a

Steps to Reproduce

this is specific to my environment and happens randomly when claude tries to commit.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

unclear

Claude Code Version

2.1.81 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

WSL (Windows Subsystem for Linux)

Additional Information

_No response_