[docs] Add CLI options to docs via `sphinx-argparse`. Update FAQs

[christinehc]

Changelog:

• 2 new FAQs have been added
• Docs pages now include all CLI options using sphinx-argparse for automatic parsing. (This adds mock as a dependency in order to bypass module imports.)
• requirements.txt was out of date and has been updated (though all requirements are currently commented out as they are not currently being used in the package setup)
• The CLI itself has been updated for better formatting of help messages and adherence to the Snakemake CLI (help messages, for instance, are now fully copied over).

[christinehc]

Note: these are minor changes that only affect the readthedocs pages.

Feel free to add suggestions for more troubleshooting questions to add to the FAQs. I've tagged @jjacobson95 and @abbyjerger in particular for this! :)