Rename preanalysis, refinediag, and analysis names

[ceblanton]

Is your feature request related to a problem? Please describe.
None of us like the current names for the plugins: preanalysis, refinediag, and analysis. They do not describe the phase of the plugin and give the impression that the workflow owns the analysis scripts.

Describe the solution you'd like
On 2026-4-9, we agreed on these alternative names:

first-step-user-scripts (previously known as pre-analysis)

refinediag-user-scripts (previously known as refinediag)

final-step-user-scripts (previously known as analysis)

Describe alternatives you've considered
Continue with the confusing and maligned names.

Additional context
Things that would have to be updated from this schema change: https://github.com/NOAA-GFDL/gfdl_msd_schemas/pull/54/changes

• YAML files that reference preanlaysis, refinediag, and analysis
• preanlaysis, refinediag, and analysis references in configure_script_yaml.py
• logic for setting do_refinediag and do_preanlysis in the rose_suite (since by default we are making these True) in configure_script_yaml.py
• update any relevant tests