Find TODO and FIXME Comments

Search the training materials codebase for TODO and FIXME comments to identify pending work.

Execute from repository root. See ../shared/repo-conventions.md for directory structure.

Tasks to Perform

1. Search Markdown Files

   • Use Grep to find TODO and FIXME in docs/**/*.md
   • Capture file path, line number, and full comment
   • Note context (which module/lesson)

2. Search Nextflow Scripts

   • Find TODO/FIXME in **/*.nf files
   • Distinguish between training examples and solution code
   • Note if in core examples or side-quests

3. Search Configuration Files

   • Check docs/en/mkdocs.yml
   • Check .github/**/*.yml and .github/**/*.py
   • Check CONTRIBUTING.md

4. Categorize Results

   • High Priority: Marked as FIXME, TODO(urgent), or blocking
   • Documentation: TODOs in markdown files
   • Code: TODOs in .nf or .py files
   • Configuration: TODOs in config files

5. Check Known Issues

   • Read CONTRIBUTING.md for any documented TODOs
   • Note which are tracked vs untracked

Output Format

# TODO/FIXME Report

## Summary
Total items, High priority count, by category (Documentation/Code/Configuration)

## High Priority Items
[List FIXME and urgent items with file:line and context]

## Documentation TODOs
[Group by file with line numbers]

## Code TODOs
[Group by file with line numbers]

## Recommendations
1. Immediate attention: [blocking items]
2. Next sprint: [significant items]
3. Low priority: [nice-to-haves]

## Files with Most TODOs
[Top 3-5 files]

Notes

• Use Grep with pattern TODO|FIXME (case insensitive)
• Distinguish between legitimate TODOs and example comments in training materials
• Provide actionable priorities, not just a list