While I've not had any particular issue with Claude figuring out how to interface and execute MRtrix3 commands, it's possible that it's chewing up more context window than necessary to do so.

I can envision something like __print_usage_mdreduced__, which would print reduced CLI information with less formatting: just synopsis, usage, options (moving more verbose option help strings to Description). Any more information required---e.g. description, example usages---could be accessed using __print_usage_markdown__.