Update documentation including qc, debugger, and namelist table

[apcraig]

PR checklist

• Short (1 sentence) summary of your PR:
  Update documentation including qc, debugger, and namelist table
• Developer(s):
  apcraig
• Suggest PR reviewers from list in the column to the right.
• Please copy the PR test results link or provide a summary of testing completed below.
  Ran quick suites on cheyenne with 3 compilers, all bit-for-bit. Code changes are minimal.
  https://github.com/CICE-Consortium/Test-Results/wiki/cice_by_hash_forks#2054d0984a4a0eb1293e9fd3266bf3dbbd45753e
• How much do the PR code changes differ from the unmodified code?
  • bit for bit
  • different at roundoff level
  • more substantial
• Does this PR create or have dependencies on Icepack or any other models?
  • Yes
  • No
• Does this PR add any new test cases?
  • Yes
  • No
• Is the documentation being updated? ("Documentation" includes information on the wiki or in the .rst files from doc/source/, which are used to create the online technical docs at https://readthedocs.org/projects/cice-consortium-cice/. A test build of the technical docs will be performed as part of the PR testing.)
  • Yes
  • No, does the documentation need to be updated at a later time?
    • Yes
    • No
• Please provide any additional information or relevant details below:

Also added checks for ncat, nilyr, nslyr, nblyr and modified the abort flags implementation in ice_init converting from namelist to character string to be able to identify multiple failures with the abort_list variable.

Addresses issues #441, #412, #375, #347, #166 at least partly.

[apcraig]

There are some obvious issues in the namelist tables. I'm working to fix them.

[phil-blain]

Looks good. I think both the abort changes and the updates to the doc are an imrpovement. Thanks!

[apcraig]

OK, I think the table is fixed. I took it offline to debug and review. @eclare108213, let me know what you think.

[eclare108213]

This is definitely an improvement, thank you. Just a couple of comments:

Under section 3.4.1, the second sentence copied below doesn’t make sense to me. Should there be additional wording, like "... in coupled configurations"?

Several of the variables defined in the file are not used in CICE. They exist to support the CICE model.

At the top of section 3.4.2, I suggest adding a sentence stating that the listed default value is assigned in the code if an option is not set (or not set correctly?) in the namelist input file, and is not necessarily the recommended value.

[apcraig]

Thanks @eclare108213, I have update 3.4.1 and 3.4.2 as suggested and will merge in the next day unless there are other comments. I will work on the same changes in Icepack next.

[eclare108213]

I just noticed that in the case settings table, kdyn=1 occurs twice. Please, would you remove the one that says "dynamics ON" and keep the one that says evp?

[apcraig]

@eclare108213, I'm not seeing the kdyn issue. Are you looking at the latest table?

https://cice-consortium-cice--459.org.readthedocs.build/en/459/user_guide/ug_case_settings.html#dynamics-nml

[eclare108213]

I was looking at the docs on master. Looks like you already took care of it. Thanks!