find-todo-and-fixme-comments

# 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](../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