[BUG] Plugins are re-enabled when claude-code is updated.

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?

I have installed a couple of plugins, but they are disabled.

And when claude code gets updated these plugins are re-enabled. It is annoying because some skills/tools are loaded when they shouldnt be. And then i have to cancel agent run and disable plugins again.

What Should Happen?

Disable plugin should not be abailable unless i turn on again.

Error Messages/Logs

Steps to Reproduce

1. Disable plugin
2. Update Claude code
3. Plugin should be disable, but is enabled

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.235

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Non-interactive/CI environment

Additional Information

_No response_