/restructure

Goal

Upgrade an existing project to the canonical layout while preserving data by creating a timestamped backup and normalizing directories.

Preparation

1. Gather root (project path), backup (default true), remove_nonstandard (default true), and force flags.
2. Verify the directory exists via ls "$root"; abort with actionable error if missing.
3. Load required directories/files from ../config/config.json -> standard_structure.

Execution

1. Backup (if enabled)

   if [ "$backup" = "true" ]; then
     ts=$(date +%Y%m%d_%H%M%S)
     backup_dir="$(dirname "$root")/$(basename "$root")_backup_$ts"
     cp -R "$root" "$backup_dir"
   fi
   

   Report backup path.
2. Create missing directories Loop through required list and run mkdir -p "$root/$dir" while tracking which ones were added.
3. Suggest file moves
   • Scan top-level items (excluding .git, .claude*).
   • For loose .py/.ipynb, suggest moving into codes/.
   • For figures (*.png, *.svg, *.pdf), suggest paper/figures/. Confirm before moving unless force=true.
4. Remove non-standard directories when permitted:

   if [ "$remove_nonstandard" = "true" ]; then
     # list directories not in required set + allowed hidden ones
   fi
   

   Always log deletions; skip if uncertain.
5. Refresh templates Re-render README, .gitignore, project.yml, .project-config.json using update_existing=true semantics (overwrite while keeping backups). Mention fields updated (e.g., restructure date).
6. Report Summarize backup, created dirs, removed dirs, files moved, and manual follow-ups.

Error Handling

• If copy fails due to permissions, warn and confirm whether to continue without backup.
• If user declines destructive step, skip and note outstanding work.
• Keep backups until user deletes them.

Example Reply

Restructured ~/projects/ablation-study
- Backup: ~/projects/ablation-study_backup_20250214_103255
- Created dirs: paper/manuscripts, pre/poster
- Moved scripts -> codes/, PNGs -> paper/figures/
- Removed non-standard dir: old-notes/
Templates refreshed with restructure date 2025-02-14.
Next: run /project-management:validate to confirm compliance.