Fix various documentation issues

[ZedThree]

This is a bid to try and get the number of Sphinx warnings down, to ideally start using error on warnings.

The major issue now is things like:

BOUT-dev/manual/sphinx/_breathe_autogen/file/pcr__thomas_8hxx.rst:4: WARNING: Duplicate C++ declaration, also defined at _breathe_autogen/file/pcr__thomas_8hxx:4.
Declaration is '.. cpp:function:: virtual void setCoefA (const Field2D &val)=0'.

which I think is complaining about overriding the pure virtual function. I don't know whether this is an issue with breathe or doxygen. Breathe is not super well maintained currently, so I might investigate other options.

I've fixed a massive chunk of these warnings by just not processing the .cxx files. I think this is probably reasonable, but it might involve going through and moving docstrings to the headers. That will take a little bit of time to do.

Making a draft now in case anyone has feedback or ideas on these changes.

[ZedThree]

I've discovered that the vast majority of the warnings emitted from Sphinx are due to two separate bugs in doxygen and breathe.

Things that still need doing:

• [ ] boutdata/boututils docs are still built as part of this repo, should probably build them separately
• [ ] go through every single file and make sure the docstring is in the header