docs: Update MC critique responses - all 4 complete and integrated #20

	name: Auto-Fix Code Quality

	on:
	push:
	branches:
	- paper2-sequential-gex
	- 'feature/**'
	- 'issue*'
	paths:
	- '**.py'
	- '**.md'
	- '**.yaml'
	- '**.yml'

	jobs:
	auto-fix:
	runs-on: ubuntu-latest
	permissions:
	contents: write

	steps:
	- name: Checkout Code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0
	token: ${{ secrets.GITHUB_TOKEN }}

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.10'

	- name: Install Python Dependencies
	run: \|
	pip install black isort docformatter

	- name: Run Black Formatter
	run: \|
	black src/ scripts/ tests/ --line-length=120 \|\| true

	- name: Run isort Import Sorter
	run: \|
	isort src/ scripts/ tests/ --profile black --line-length=120 \|\| true

	- name: Run docformatter
	run: \|
	docformatter --in-place --wrap-summaries=120 --wrap-descriptions=120 --recursive src/ scripts/ tests/ \|\| true

	- name: Fix Markdown Linting
	uses: DavidAnson/markdownlint-cli2-action@v16
	with:
	globs: '*/.md'
	fix: true
	continue-on-error: true

	- name: Check for Changes
	id: git-check
	run: \|
	git diff --exit-code \|\| echo "changes=true" >> $GITHUB_OUTPUT

	- name: Commit and Push Auto-Fixes
	if: steps.git-check.outputs.changes == 'true'
	run: \|
	git config user.name "github-actions[bot]"
	git config user.email "github-actions[bot]@users.noreply.github.com"
	git add -A
	git commit -m "style: Auto-fix code quality issues [skip ci]

	- Applied black formatting
	- Sorted imports with isort
	- Fixed markdown linting (MD022, MD032)
	- Fixed docstring formatting

	🤖 Automated by GitHub Actions"
	git push

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