MCP is nice, but does your agent use it without you explicitly asking it to do so?
From my experience, instructions in `.md` files aren't enough. In fact, Claude seems to prefer the shell over even its own built-in tools (e.g. `read`, `edit` etc.) See: https://github.com/anthropics/claude-code/issues/19649. It's like an old dog that needs to be tricked to learn new tricks.