dvc: regroup all command options/flags [quality]

[jorgeorpinel]

As suggested in treeverse/dvc.org#3345 and implemented for run, repro, and stage add in #7524, we could come up with a logical way to present options/flags. The criteria we came up with so far is basically:

1. Put general/misc. short options/flags first (with -hqv)
2. Make groups of args based on functionality e.g. stage add -dDp (all dependency-related)
3. Order these arg groups in some logical way e.g. chronologically (deps, then outs) or by most-needed-first.
4. Put remaining misc. args at the end.

[jorgeorpinel]

Cc @dberenbaum @omesser

[dberenbaum]

@skshetry What do you think about this as part of our UI guidelines in #5392?