Fill out documentation

[standage]

• Filled out the user manual. Some redundancy with the demo.
• Filled out docstrings for the Python API.
• Filled out descriptions for the CLI.

Once this branch is merged, the docs at ReadTheDocs will be updated. But for evaluation purposes, run make doc and open docs/_build/index.html locally.

Partially satisfies #107.

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• [x] Changes are clearly described above
• [x] Any relevant issue threads are referenced in the description
• Any new features are tested (see docs/DEVEL.md for details)
• Substantial changes are documented in CHANGELOG.md (see https://keepachangelog.com/en/1.0.0/)

[standage]

Still making a few last-minute changes here to synchronize the CLI and API, so let's hold off on review until further notice.

[standage]

Ok, as noted in #107, there is still some work to be done synchronizing the CLI and API docs, but it's all filled out for now and I think our time would be better invested elsewhere at the moment. So this is really ready for review now!