Documentation cleanup

My idea here:

• Make every output optional. This way the full list of outputs is specified in the config.
• Allow the variable doc generation to read the config file rather than the h5 outputs (but keep the h5 reading as well).
• Clean up the variable names a bit.

The last step is pretty annoying without the former steps, since the doc generation scripts previously relied on producing an h5 file.

I had a more elaborate idea to move all the doc generation to the input files, thus breaking the dependence on the outputs in the CI. The problem is that I'd have to introduce CI tests to verify that the output is actually what is specified in the config file. I'm leaving that for later work since I should probably just focus on cleaning up the documentation. There's a script dump-output-from-h5 that I'll eventually complement with dump-output-from-config and diff in the CI, if I ever get to this next step.