[Bug] Claude Code not following user instructions consistently

Bug Description
For some reason, Claude Code seems to be struggling to follow some of my instructions, even though they're very clearly documented. This seems to be a regression, it didn't use to ignore so many of my instructions like this.

Environment Info

• Platform: linux
• Terminal: pycharm
• Version: 2.0.61
• Feedback ID: 214c3fce-211f-4dbb-8444-39307cd9716c

Errors

[{"error":"Error: Shell 9abd78 is not running, so cannot be killed (status: failed)\n    at call (/$bunfs/root/claude:2839:1840)\n    at async nF9 (/$bunfs/root/claude:3117:16948)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-09T00:21:36.061Z"}]