The AI definitely gets confused when there is a lot of stuff happening. It helps if you try to make the commands as easy as possible. Like, change 'make' so that '-j8' is default, or add scripts like make-check.sh that does 'make -j check', or add an MCP server that has commands for the most common actions (tell the AI to write an MCP server for you).

Hooks would probably help, I think you could add a hook to auto-reject the bot when it calls the wrong thing.