It's shocking how shitty claude code CLI app is - config is brittle shit (setting up a plugin LSP is searching through GitHub issues and guessing which parameters you messed up), hooks render errors in the app when there are none and the permission harness is barely documented, zero customization options (would you like the agent config come from a different folder than source root ? nope). Going through gihub issues, same issue you hit has been open since beginning of 2025 and ignored - their issues are /dev/null - it's basically a user forum.