find-todo-and-fixme-comments

name	Find TODO and FIXME Comments
description	Search markdown files, Nextflow scripts, and config files for TODO/FIXME comments, categorize by priority, and provide actionable recommendations. Use when you need to identify pending work or track technical debt.

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