Minor housekeeping updates

[rly]

Motivation

• Update ruff action to non-deprecated one
• Update github-app-token action to official github one
• Remove requirements-min.txt in favor of an optional dependency group in pyproject.toml and update docs accordingly
• Update pyproject.toml license key to correct format
• Add back ruff mccabe complexity check which was accidentally removed in transition to ruff
• Refactor some code to reduce complexity and added complexity check exceptions in other code
• Clean up ruff config

How to test the behavior?

Show how to reproduce the new behavior (can be a bug fix or a new feature)

Checklist

• Did you update CHANGELOG.md with your changes?
• Does the PR clearly describe the problem and the solution?
• Have you reviewed our Contributing Guide?
• Does the PR use "Fix #XXX" notation to tell GitHub to close the relevant issue numbered XXX when the PR is merged?

[codecov]

Codecov Report

Attention: Patch coverage is 92.75362% with 5 lines in your changes missing coverage. Please review.

Project coverage is 91.63%. Comparing base (5858ee0) to head (f07cf92).
Report is 1 commits behind head on dev.

Files with missing lines	Patch %	Lines
src/hdmf/common/resources.py	90.32%	2 Missing and 1 partial ⚠️
src/hdmf/spec/spec.py	90.47%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #1246      +/-   ##
==========================================
+ Coverage   91.56%   91.63%   +0.07%     
==========================================
  Files          42       42              
  Lines        9552     9550       -2     
  Branches     1928     1920       -8     
==========================================
+ Hits         8746     8751       +5     
+ Misses        523      521       -2     
+ Partials      283      278       -5     

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[mavaylon1]

@rly overall this looks good. There are coverage gaps. If you are okay with that, then I will approve.

[rly]

Looking closely at the coverage report, I see that all the lines that now lack coverage had previously lacked coverage. We can add the missing tests in a separate PR, but I think that should not need to block this one.