[develop]: Minor updates to documentation

[gspetro-NOAA]

DESCRIPTION OF CHANGES:

• Added Intersphinx links to hpc-stack docs & removed hpc-stack submodule (NOTE: the hpc-stack-mod is ONLY used to link the docs and its removal should not affect any SRW code)
• Put tables into “tables” directory instead of directly under "source"
• Updated stochastic physics link
• Remove glossary duplicates (sometimes two terms, singular and plural, are connected with one definition)
• Updated Quickstart to reflect python workflow

Type of change

• This change requires a documentation update (all documentation)

TESTS CONDUCTED:

None required. Documentation updates.

• hera.intel
• orion.intel
• gaea.intel
• jet.intel
• NOAA Cloud (indicate which platform)

DEPENDENCIES:

None.

DOCUMENTATION:

All documentation.

ISSUE:

Resolves Issue #379

CHECKLIST

• [X ] My code follows the style guidelines in the Contributor's Guide
• I have performed a self-review of my own code using the Code Reviewer's Guide
• I have commented my code, particularly in hard-to-understand areas
• My changes need updates to the documentation. I have made corresponding changes to the documentation
• My changes do not require updates to the documentation (explain).
• My changes generate no new warnings
• New and existing tests pass with my changes (no tests required since the PR is documentation)
• Any dependent changes have been merged and published (N/A)

[danielabdi-noaa]

It maybe good to mention that if the user has a shell script config file, he can either do any of the following

a) use it as is by changing the following parameter in config_defaults.yaml

EXPT_CONFIG_FN: "config.sh"

b) or convert it to yaml with

./config_utils.py -c $PWD/config.sh -t $PWD/config_defaults.yaml -o yaml >config.yaml

[gspetro-NOAA]

@danielabdi-noaa I think this is a good thing to mention, but I will probably wait to add it to the main Build/Run chapter when I make those updates. The Quickstart chapter is supposed to be as succinct as possible, so I just show one way to run the workflow and refer the users to other chapters for additional options.

[danielabdi-noaa]

Sounds good! Just one more thing I forgot to mention: The user can check a validity of a given config file by comparing it against config_defaults.yaml. For example

$ ./config_utils.py -c $PWD/config.yaml -v $PWD/config_defaults.yaml 
SUCCESS

If there is an invalid entry, you will get something like

$ ./config_utils.py -c $PWD/config.yaml -v $PWD/config_defaults.yaml
INVALID ENTRY: ACCPP_PHYS_SUITE=FV3_GFS_v15p2
FAILURE