Comment by smallnamespace

Three facts to consider:

1. CLAUDE.md is not part of the system prompt

2. The Claude Code system prompt almost certainly gives directions about how to deal with MCP tools, and may also include the list of tools

3. Instruction adherence is higher when the instructions are placed in the system prompt

If you put these three facts together then it’s quite likely that Claude Code usage of a particular tool (in the generic sense) is higher as an MCP server than as a CLI command.

But why let this be a limitation? Make an MCP server that calls your bash commands. Claude Code will happily vibe code this for you, if you don’t switch to a coding tool that gives better direct control of your system prompt.