Documentation: adding entire directory structure to doxygen

[aniabrown]

It looks like the CPU and GPU folders need to be added to the doxygen config as these files are not currently showing up

[aniabrown]

I updated the doxyconf file to include files in those directories in f5cf4a5. However, I couldn't find a way for the directory structure to be kept in the list of files in https://quest-kit.github.io/QuEST/files.html. Also, where there are multiple implementations of a function, the source code of the serial cpu implementation will be the one linked from header files etc -- we may consider generating a different version of the documentation for each architectures (would only be useful for developers).

[TysonRayJones]

Should we avoid making these changes on master? I worry it could break the doc on https://quest.qtechtheory.org/docs/ which has links to Doxygen keys.
Note there are no public-facing functions in the backend, so this doesn't expose more doc to a user.

Note also (as mentioned on the 18th) there's some problem with the repo, where pull requests are cloning all 200 of previous commits - master is already ahead of dev! We should fix this asap before making any more big commits, especially to master.

[aniabrown]

Looks like the links are still working as I only made changes to the file list page, which as far as I can tell isn't referenced in https://quest.qtechtheory.org/docs/. I take your point though -- I'm happy to do updates to files outside the QuEST library directory on the develop branch as well from now on. (Let me know if you're still worried about this one and I can revert it as well).

Will look into the pull request issue.