Update documentation and add quick-start guide

[WalterKolczynski-NOAA]

Description

Updates stale portions of the User's Guide and adds a Quick-Start guide and native AWS cluster build instructions.

The new Quick-Start guide walks users through setting up, building, and running the C48_ATM test case with generate_workflow. It is intended to be a new user's first contact with running global workflow.

The User's Guide is given a thorough revision. The most obvious changes are the inclusion of some new tables, including an update to the job description table to cover all existing jobs with new columns added denoting which forecast systems use the jobs. System configurations were determined based solely on the corresponding tasks script. This has resulted in some systems being marked for jobs that are not actually run due to vestigial code from copying existing code to make new systems. The table is also separated out from the GFS page since it now covers all systems.

Another big change is the addition of system description pages for GEFS and SFS, as well as an overhaul of the GFS. These are patterned loosely on what is there for GCAFS, though as yet not as thorough.

Resolves #4559
Resolves #4560
Resolves #4561

Type of change

• Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

• Is this change expected to change outputs (e.g. value changes to existing outputs, new files stored in COM, files removed from COM, filename changes, additions/subtractions to archives)? NO
• Is this a breaking change (a change in existing functionality)? NO
• Does this change require a documentation update? YES
• Does this change require an update to any of the following submodules? NO

How has this been tested?

Review of PR documentation build on RTD.

Documentation only: no HPC testing requried.

Checklist

• Any dependent changes have been merged and published
• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have documented my code, including function, input, and output descriptions
• My changes generate no new warnings
• New and existing tests pass with my changes
• This change is covered by an existing CI test or a new one has been added
• Any new scripts have been added to the .github/CODEOWNERS file with owners
• I have made corresponding changes to the system documentation if necessary

[WalterKolczynski-NOAA]

Still waiting on one small section for the native AWS cluster build instructions for establishing a lustre file system, but otherwise this is ready.

Could use a thorough look-over, as I'm going a bit cross-eyed from looking at it so much the last few days.

[Copilot]

Pull request overview

This PR reorganizes and refreshes the Sphinx/RTD documentation, adding a new Quick Start path for first-time users and expanding platform/system coverage (including native AWS cluster build guidance) while standardizing the User’s Guide structure and content.

Changes:

• Adds a new quick_start.rst walkthrough for running a low-resolution GW test case via the case/YAML workflow generator.
• Reworks the User’s Guide into docs/source/user_guide/ with new system overview pages (GFS/GEFS/SFS), a consolidated job description table, and updated HPC/platform guidance.
• Adds/updates contributor documentation, including new wave component documentation and a detailed CI/CD infrastructure reference.

Reviewed changes

Copilot reviewed 27 out of 46 changed files in this pull request and generated 20 comments.

Show a summary per file

File	Description
docs/source/User_Guide/view.rst	Removes legacy View Output page (superseded by lowercase user guide).
docs/source/user_guide/view.rst	Adds updated “View Experiment output” page with hierarchical output structure.
docs/source/user_guide/start.rst	Adds anchors/spacing tweaks for cron/scrontab section.
docs/source/user_guide/sfs.rst	Adds SFS system overview page.
docs/source/User_Guide/setup.rst	Removes legacy experiment setup page (superseded by lowercase user guide).
docs/source/user_guide/setup.rst	Adds revised experiment setup instructions (including case/YAML method).
docs/source/user_guide/setup_run_pworks.rst	Updates ParallelWorks CSP run instructions formatting/headings.
docs/source/user_guide/run_hpc.rst	Updates “run on supported HPC” landing page; adds pointer to quick start.
docs/source/user_guide/plot_output.rst	Adds initial plotting guidance (RadMon) placeholder for forecast plotting.
docs/source/user_guide/monitor_rocoto.rst	Updates Rocoto monitoring doc formatting/capitalization.
docs/source/user_guide/job_descriptions.rst	Adds consolidated job description table across systems.
docs/source/user_guide/init.rst	Updates initial conditions documentation and formatting for examples.
docs/source/user_guide/index.rst	Updates User’s Guide toctree and adds new pages (AWS build, system pages, job descriptions).
docs/source/user_guide/hpc.rst	Replaces capabilities matrix with new table; updates restricted-data guidance/anchors.
docs/source/user_guide/globus_arch.rst	Minor clarification/formatting updates for Globus-to-HPSS instructions.
docs/source/user_guide/gfs.rst	Adds new GFS system overview page.
docs/source/User_Guide/gfs_jobs.rst	Removes legacy GFS jobs page (content redistributed/updated).
docs/source/user_guide/gefs.rst	Adds new GEFS system overview page.
docs/source/user_guide/gcafs.rst	Significant restructuring/formatting updates for GCAFS documentation.
docs/source/user_guide/errors_faq.rst	Adds a new FAQ entry with a workflow setup failure example.
docs/source/user_guide/configure.rst	Adds a “Configure Run” page with a switch/reference table.
docs/source/user_guide/components.rst	Updates component descriptions and adds dump archive anchoring and AWS S3 reference.
docs/source/user_guide/clone.rst	Updates clone/build instructions, adds build-options tables, improves cross-references.
docs/source/user_guide/background.rst	Refreshes background/organization text and adds AWS EC2 cluster doc mention.
docs/source/user_guide/aws_cluster_build.rst	Adds native AWS ParallelCluster/Packer-based cluster build instructions (currently incomplete in one section).
docs/source/quick_start.rst	Adds Quick Start guide for building/running a first C48_ATM test case.
docs/source/index.rst	Adds Quick Start to top-level docs and updates guide toctrees to lowercase paths.
docs/source/contributor_guide/wave.rst	Adds contributor-facing wave component documentation.
docs/source/contributor_guide/testing.rst	Updates cross-references to the new user guide paths.
docs/source/contributor_guide/index.rst	Adds a contributor guide index/toctree.
docs/source/contributor_guide/development.rst	Updates CI guidance and modernizes code-block formatting and user-guide links.
docs/source/contributor_guide/ci_cd_pipeline.rst	Adds a comprehensive CI/CD pipeline infrastructure reference (GitHub↔GitLab↔RDHPCS).

Comments suppressed due to low confidence (5)

docs/source/user_guide/run_hpc.rst:9

• This :doc: link target is reversed/invalid. The first part should be the link text (optional) and the second should be the document path; as written it will not resolve to the quick start page.
  docs/source/user_guide/errors_faq.rst:14
• This section title says an AttributeError about __frozen, but the example traceback shows a KeyError: 'PTMP'. The mismatch makes the FAQ hard to search and can mislead users diagnosing the error.
  docs/source/contributor_guide/testing.rst:789
• This doc link points to ../user_guide/gfs_jobs, but that document is not present in docs/source/user_guide/ (it was replaced by gfs.rst and job_descriptions.rst). This will be a broken link in the rendered docs.
  docs/source/user_guide/gcafs.rst:68
• This path omits the dev/ prefix; Rocoto task definitions are under dev/workflow/rocoto/ in this repo. As written, the documentation points users to a non-existent location.
  docs/source/user_guide/gcafs.rst:70
• The reference label is .. _job_descriptions: (without a leading underscore) in job_descriptions.rst. Using :ref:_job_descriptions`` will create a broken reference in the built docs.