[WIP] run_neon fixes and improvements

[samsrabin]

Work in progress!

Subject to force pushes!

Description of changes

Resolves some bugs and improves some messaging. Also, two new options:

• --no-inputdata-check option implies --setup-only but skips the check/download of input data.
• --xmlchange option allows user to specify xmlchange settings to apply. E.g., --xmlchange CLM_CO2_TYPE=constant,CCSM_CO2_PPMV=850.

Specific notes

Contributors other than yourself, if any: None

CTSM Issues Fixed:

• Resolves run_neon --overwrite is ignored #2884
• Resolves run_neon --setup-only is ignored #2885

Are answers expected to change (and if so in what way)? No

Any User Interface Changes (namelist or namelist defaults changes)? No

Does this create a need to change or add documentation? Did you do so? No

Testing performed, if any: Manual testing.

[wwieder]

@samsrabin I really appreciate you work here, but also note that all of this is subject to change with #2406 when we integrate the run_towers workflow that @TeaganKing developed and that's waiting for input from @ekluzek . I might hold off making quality of life improvements in run_neon until after we have the plumber2 capability merged.

[samsrabin]

Good point, @wwieder. For now I'll continue to develop this branch just for my own benefit (using it in a demo tomorrow), and after #2406 is merged I can see if anything here would still be useful.

[ekluzek]

@samsrabin just pinging you on this to see if this is something you might be able to do before the release? Also note that #2406 is merged to b4b-dev. So this should probably be merged or re-based to b4b-dev and merged with that, if that's possible for this one.

[samsrabin]

Before the ctsm6.0 release? Yes, I'd still like to get this in before that.

[wwieder]

Sounds good to me, @samsrabin have a look after we merge b4b-dev? I think then #2406 will be on main.

[samsrabin]

Closed because I renamed this branch. Will make a new PR.