Cursor has basically run into this exact thing. It figured out it can read .env files by running other tools despite the file being "blocked": https://github.com/getcursor/cursor/issues/2546
I ran into this issue, I built my own bash and SSH MCP server. In my first iteration I did not quite trust Claude yet so I limited the commands it was allowed to run in Bash. But I gave it access to Python, so any time it ran into a limitation it ended up using python to work around it. It's exceedingly good at problem solving.
I Eventually learned to trust Claude, and just gave it access to everything. It's crazy how useful having AI do tasks for you like setting up servers, configuring them etc (one exapmple, I asked claude to create a webhook for my deployment pipeline, and it wrote the shell script, and did the server side configuration in 1-shot. I did't have a github tool so I did that manually in the UI)
