Python: Remove one of three filesystem structures

[Lestropie]

Downstream of #2920.

Follows discussion in #2964.

---

1. Currently on dev:

   1. C++ commands must be defined using a single file cmd/cmdname.cpp
   2. For Python commands there are three possible arrangements:
      1. A single file python/mrtrix3/commands/cmdname.py.
      2. A file python/mrtrix3/commands/cmdname/cmdname.py, to facilitate inclusion of other files within a sub-directory specific to that command.
      3. Two files python/mrtrix3/commands/cmdname/usage.py and python/mrtrix3/commands/cmdname/execute.py, which define the relevant entry points.

2. It is being proposed in #2964 that:

   1. For C++ it should be possible to have either:
      1. A single file cmd/cmdname.cpp.
      2. A file cmd/cmdname/cmdname.cpp, to facilitate inclusion of other files within a sub-directory specific to that command.

My proposal here is: especially if #2964 is implemented, providing support for 2.i.b., then it makes sense to remove support for 1.ii.c..

That way the supported filesystem structure per command will be consistent between the two languages. As shown by the content of this PR, there is little to no sacrifice in doing so; conversely there's the benefit of any communication around permissible filesystem structures likely being simpler.

[github-actions[bot]]

clang-tidy review says "All clean, LGTM! :+1:"

[github-actions[bot]]

clang-tidy review says "All clean, LGTM! :+1:"