[WIP] Update documentation

[fiona-naughton]

Overhaul of the documentation.

The main changes are:

• Splitting up the current documentation
• Adding additional documentation such that all files (bar some related only to linting) should be covered at least in passing
• Adding a new "files" table that lists all all the files, a description, and an assessment on whether they are

The files table in particular may be contentious. The thought is to try make it clear to users on one hand which files are "important" or which they could theoretically remove if they prefer a slimmer package, and on the other to point out which files they'll need to edit and which they can just 'ignore'; hopefully I haven't over complicated it.

Still To Do, though these need not all happen in this PR:

• General formatting adjustments
• Extend the existing framework for generating the file skeleton/descriptions and use that to make the file table instead, to keep things a bit tidier?
• Fancify the files table - allow sorting? colour coding? navigation that more closely matches an actual file tree structure?
• Links to the MDAKits docs (inc. the example rmsf kit tutorial)
• I've currently not added explanations for linting-associated files