Removes group parsing from command ref domain, instead relying on a 'groups' object in the cmds.json file.
`docs/source/cmd` is no longer ignored or cleaned.
Add `doc_string` field to `Pass` constructor
Add `docs/util/newcmdref.py` to contain command domain
Update `docs/util/cmdref.py` with `cmd:usage` and `cmd:optiongroup` for describing commands.
Functional, but WIP.
