JP-3574: fix stage 2 pipeline steps not respecting output_file parameter

[emolter]

Resolves JP-3574

Closes #8354

This PR addresses a bug where the spec2pipeline and image2pipeline did not respect the output_file parameter when it was set by the user. Small documentation updates also clarify that associations generally should not have multiple rate or rateints files in them.

Checklist for maintainers

• added entry in CHANGES.rst within the relevant release section
• updated or added relevant tests
• updated relevant documentation
• added relevant milestone
• added relevant label(s)
• ran regression tests, post a link to the Jenkins job below.
  How to run regression tests on a PR
• Make sure the JIRA ticket is resolved properly

[emolter]

regression test run started here

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.77%. Comparing base (2fb073e) to head (d3e4ae2).
Report is 18 commits behind head on master.

❗ Current head d3e4ae2 differs from pull request most recent head af6cbcf. Consider uploading reports for the commit af6cbcf to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #8368      +/-   ##
==========================================
+ Coverage   75.31%   75.77%   +0.46%     
==========================================
  Files         474      476       +2     
  Lines       38965    39442     +477     
==========================================
+ Hits        29345    29887     +542     
+ Misses       9620     9555      -65     

Flag	Coverage Δ		*Carryforward flag
nightly	77.63% <ø> (+0.29%)	⬆️	Carriedforward from 2fb073e

*This pull request uses carry forward flags. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[emolter]

Hopefully fixed regression test failures, new Jenkins run started here

[emolter]

one more regtest attempt here

edit: after problems with Jenkins were resolved, regtest run here.

Regtest run had some failures in MIRI imaging that I believe were unrelated

[hbushouse]

All failures in the last regtest run were benign.