athena.py: restore --help for flags

Restore the ability to print the help message for flags when using athena in CA-mode. This was broken after the recent refactoring and making the use of --CA redundant. The command line interface is now:

  athena --help flags   # prints all flag categories
  athena --help Input   # help for flags within one category

No changes if --help is used directly on a CA script (as opposed to running it through athena).

cc @will @wlampl