fixes reading dimensions for Omega decomposition and unused dimensions

[philipwjones]

The original Decomp read only legacy MPAS mesh files with older dimension/variable names. This adds support for the newer names in Omega conventions. Additional changes modify the behavior when missing variables or dimensions are encountered. Defined dimensions that are missing or unused in input files are ignored during the file read. Also, error or warning messages for missing dimensions or variables at the base IO level are now suppressed and the error is passed to the calling routine to determine the proper behavior. This eliminates warnings for harmless situations that can cause confusion and unnecessary output in the log file.

All unit tests pass on Chrysalis/Intel.

Checklist

• Testing
  • A comment in the PR documents testing used to verify the changes including any tests that are added/modified/impacted.
  • CTest unit tests for new features have been added per the approved design.
  • Polaris tests for new features have been added per the approved design (and included in a test suite)
  • Unit tests have passed. Please provide a relevant CDash build entry for verification.
  • Polaris test suite has passed

fixes #172, fixes #173

[xylar]

Thanks very much for getting to this so quickly, @philipwjones! At a glance, it looks very good. I'll test it out tomorrow in Poalris.

[xylar]

@philipwjones, this is great!

I did a merge with develop (and did my best to resolve the resulting conflict).

I then tested this with the Polaris branches I have in progress to make use of this:
E3SM-Project/polaris#231
E3SM-Project/polaris#249
E3SM-Project/polaris#242

Neither manufactured solution nor cosine bell are working quite right yet but the mechanics are finally all in place. With this PR, I am now able to translate both dimension and variable names between MPAS-Ocean and Omega conventions, perform forward runs with both models, translate the dimensions and variables back, and perform analysis and visualization (which then shows that we still have some work to do!).

I performed my tests on Chrysalis with Intel.