Improve fortran-src CLI

[raehik]

A recent issue (#169) indicated to me that the current fortran-src CLI has some unexpected behaviours with respect to options and commands, that might make it tough to get started with the tool.
I think a large part of the issue is down to all the options and commands being available to the user at all times, and relevant ones being used. Designing the CLI data types so that each command stores exactly its available options is more tedious, but would let the CLI be more discoverable (optparse-applicative has nice behaviour with respect to subcommand help).

[raehik]

I'm not sure how important the fortran-src CLI is viewed as, but it certainly is used (by myself too). I've got a template from one of my recent projects where I had success with the highly explicit/tedious style.