fix: Adopt some more opinionated ruff rules, manual resolutions

[effigies]

Follow-up to #492. This is not 100% manual, but it was difficult to separate out the manual from the automatic without parsing out exclusions.

This could stand a review.

[codecov]

Codecov Report

Attention: Patch coverage is 86.04651% with 6 lines in your changes missing coverage. Please review.

Project coverage is 84.16%. Comparing base (b4a01f6) to head (06b9bab).

Files with missing lines	Patch %	Lines
sdcflows/workflows/base.py	0.00%	2 Missing ⚠️
sdcflows/cli/parser.py	50.00%	1 Missing ⚠️
sdcflows/interfaces/reportlets.py	50.00%	1 Missing ⚠️
sdcflows/interfaces/utils.py	66.66%	1 Missing ⚠️
sdcflows/workflows/fit/base.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #493      +/-   ##
==========================================
+ Coverage   84.09%   84.16%   +0.06%     
==========================================
  Files          30       30              
  Lines        2880     2873       -7     
  Branches      374      372       -2     
==========================================
- Hits         2422     2418       -4     
+ Misses        384      381       -3     
  Partials       74       74              

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