[develop]: Add linkcheck & RTD theme; re-organize documentation

[jdkublnick]

Description of changes

• Added blue RTD theme
• Added make linkcheck option
• Re-organized to correspond with other organization of UFS apps
• Renamed docs to doc to comply with NCO Implementation Standards
• Added requirements.in file to automatically generate full list of dependencies for requirements.txt.
• Add contribution guidelines (HAFSCodeContributionGuidelines.rst) to summarize information in documents and slides that can only be accessed by NOAA & affiliates.
• Remove several links that are not accessible to the public.

Issues addressed (optional)

• Fixes #262
• Docs working
• The build:os key is now required in .readthedocs.yml, so all doc builds will fail until that is updated

Dependencies

N/A

Contributors (optional)

N/A

Tests conducted

None required. Docs build without error locally. Docs also build successfully on RTD from my fork and can be viewed here: https://jdk-hafs.readthedocs.io/en/text-us-64/

Application-level regression test status

None required

[gspetro-NOAA]

@jdkublnick Could you rename the docs directory to doc? It seems that that change somehow got reverted. You'll also need to update the path(s) in .readthedocs.yaml.

[gspetro-NOAA]

@jdkublnick In line 40 of GitHubBasicSteps.rst, make linkcheck is saying there is a redirect to https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project. The forking link that's causing the redirect message should be replaced with this updated "contributing to a project" link.

[gspetro-NOAA]

@jdkublnick The Makefile needs to be updated to match the content in the SRW App and Land DA. Currently, make linkcheck seems to work without explicitly specifying a linkcheck option, but there is no make doc option, as there is in the SRW/Land DA repos that would run both make html and make linkcheck together. In general, we want to override any default behaviors and specify exactly what we want to happen when make linkcheck or make doc are run.

[gspetro-NOAA]

@KathrynNewman @BinLiu-NOAA Most of these changes are aesthetic, but it would be helpful if you could take a look at HAFSCodeContributionGuidelines.rst since that is completely new and summarizes the code contribution process. Much of it is derived from the process we use on other UFS repositories, and it is intended to replace some of the internal documents/slides that we removed. That said, you are more familiar with the HAFS code contribution process, so it would be good to have your eyes on that doc to be sure that everything in there is true for HAFS, specifically.

[BinLiu-NOAA]

@gspetro-NOAA and @KathrynNewman, with that, I will go ahead and Squash and Merge this PR then. Thanks!