Make command line arguments more better

Original MR

This is my attempt to clean up the command line interface a bit. There were a few unused arguments, and a few others that were too verbose given how often they are used.

I like reusing Athena common option parsing, but I think breaking off the argument parser creation is justified for a few reasons.

• There should always be input files, so it's weird that this argument was optional. I've made it positional for now, but I could be convinced to go back to making it a "required optional argument".
• The threads and processes arguments weren't used anywhere in our code, so I hid them.
• Our required --runConfig argument was listed way down the help, I moved it earlier.
• There were some obvious places that the standard Athena parser could use help, e.g. using choices could be used more, which I should port to Athena.
• There are some options that are just weirdly implemented, but which we probably can't change for backward compatibility reasons. In particular --config-only takes an argument which ends up being the name of a pickle file that stores the configuration. There's no obvious way to use this file. I renamed it --stop-after-config and made it write the file to /dev/null.

Note that I keep the same names for the args namespace object, so it's still compatible with the Athena flag filling.

I'm also wanting to make the --runConfig option optional, since I always use the same one for quick tests and get annoyed with having to specify it.

Todo:

• Remove unused arguments from the help string
• Make filesInput mandatory
• Make --runConfig optional

Things that should be in another MR

Since I need a few things to work in the same branch I started piling in stuff that might have been better in other merge requests:

• I'm removing the --allow-missing-ptag option: I don't see it used anywhere anyway. This should close #26 (closed).
• Make the --outFile argument optional
  • Make sure this is still being produced in the unit tests.
• Remove unused --allow-no-ptag
• Everything from !134 (closed)