Support ACME short-term archiving

[milenaveneziani]

When ACME short-term archiving will be turned on, the history files will be stored in component-specific archive directories. In particular, if $rundir is the root run directory, the files we will need for MPAS-Analysis to work will be archived in the following subdirectories:

1. $rundir/ocn/hist will contain all mpaso.hist files
2. $rundir/ice/hist will contain all mpascice.hist files (perhaps we should suggest this to be changed to $rundir/sea-ice/hist?)
3. the restart, namelists and streams files should remain in the $rundir/run directory, as is currently.

Therefore, we will need to make sure that, when short-term archiving is activated, the ocean and ice directories point to the right place.

Note that, in the ACMEPreAndPostProcessing csh scripts, we currently have a user-defined flag for short-term archiving.

[xylar]

@milenaveneziani, I think the solution is fairly simple here. Under [input], we need change baseDirectory to be one directory down from where it is in all the example config files and we need to add something likerunSubdirectory, oceanHistorySubdirectory and seaIceHistoryDirectory. I'm not attached to these names. Then, we probably want to have them all default to run but in ACME/PreAndPostProcessingScripts, we would change them (if short-term archiving is on) to point to these directories.

We could even have the scripts fall back on the runSubdirectory if they don't find what they need in oceanHistorySubdirectory (etc.) or even have them just search in both always.

[milenaveneziani]

yes, I agree something simple should work. I will try to implement this option within the next submodule update.

[xylar]

I should note that #128 would make this quite a bit simpler because it puts quite a bit of common code in the base class that all analysis tasks derive from. The setup_and_check method would be the place where these changes would go:
https://github.com/MPAS-Dev/MPAS-Analysis/pull/128/files#diff-f4c01dd9c50e825c99d4d138d9001e07R62

If we make this change before merging #128, there will be quite a bit of redundant work that will have to be undone in #128. That's fine if the change is needed before we can get around to merging #128.

[xylar]

@milenaveneziani, I'm working on this one today.

[milenaveneziani]

Thanks @xylar, and sorry if I didn't reply to this before.
So, I am not sure if the short-term archiving capability will be available in the next couple of weeks or not.. I could ask around.

[xylar]

Addressed by #153