Refactor: Data directory structure, R2 backup, and fixed branch strategy in workflows

[marcarl]

Summary

This PR modernizes the SFS workflow architecture with three major improvements:

1. Cleaner data/ directory structure for all committed files
2. Cloudflare R2 as permanent backup for JSON files
3. Fixed branch strategy to eliminate branch proliferation

Changes

📁 New Directory Structure

• data/sfs_json/ - Source JSON files (committed to git + backed up to R2)
• data/md-markers/ - Markdown with selex tags (committed to git)
• output/ - Generated files (ignored in git, HTML goes to R2)

☁️ Cloudflare R2 Backup

• All JSON files synced to R2 for permanent storage
• Provides redundancy and protection against git issues
• html-export uses smart fallback: git first, R2 if unavailable

🔄 Fixed Branch Strategy (NEW)

• Eliminates branch proliferation: Single branch workflow-artifact-data instead of timestamped branches
• Automatic PR lifecycle: Old PR closed, new PR created on each update
• Workflow coordination: Both fetch-sfs and upcoming-changes use same branch
• Temporal branches unchanged: Date-range branches for historical commits remain separate

⚙️ Configurable Git Commits

• enable_git_commit (default: true) - Enable/disable git commits
• branch_name (default: workflow-artifact-data) - Configurable branch name

Benefits

✅ Better organization - All source data in data/, generated in output/
✅ Permanent backup - JSON files in both git and R2
✅ No branch cleanup needed - Single fixed branch, reused on each run
✅ Simplified coordination - All workflows use same branch
✅ Clear naming - md-markers shows selex tags included

Before/After

Aspect	Before	After
Branch strategy	New timestamped branch each run	One fixed branch, reused
Branch cleanup	Manual (never done)	Automatic (single branch)
Workflow coordination	Separate branches	Shared fixed branch
PR management	Many PRs accumulate	One PR per update cycle

Testing

• ✅ YAML syntax validated
• Ready for manual workflow trigger to test fixed branch behavior
• Temporal workflows remain independent and unaffected