[Sync] Reorganize output directories + deduplicate snakefiles + bugfixes #1

	name: verify-no-new-public-commits

	on:
	pull_request:
	branches:
	- main
	push:
	branches:
	- main

	env:
	PUBLIC_REPO_URL: https://github.com/Arcadia-Science/ProteinCartography

	jobs:
	verify-no-new-public-commits:
	runs-on: ubuntu-latest
	# only run this job in the private repo
	# (but do not check the repo owner, because forks will have a different owner)
	if: github.event.repository.name == 'ProteinCartography-private'
	steps:
	- name: Checkout the repo
	uses: actions/checkout@v4
	with:
	# fetch the full history so that we can check for new commits
	fetch-depth: 0

	- name: Add and fetch the public repo
	run: \|
	git remote add public ${{ env.PUBLIC_REPO_URL }}
	git fetch --all

	- name: Check for new commits in the public repo
	run: \|
	NEW_COMMITS=$(git log --oneline --no-merges ..public/main)
	if [ -z "$NEW_COMMITS" ]; then
	echo "There are no new commits in the public repo."
	exit 0
	else
	echo -e "This action failed because there are new commits in the public repo:\n\
	$NEW_COMMITS\n\n\
	Please use the \"open-public-sync-pr\" GitHub Action to merge them \
	into the private repo before merging new PRs."
	exit 1
	fi

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