organize

name	organize
description	Audit project structure, align layout to conventions, and archive superseded content. Use for cleaning up folders, standardizing layout, or preparing a workspace before committing.

Organize Skill

Audits any project directory, aligns it to a consistent structural convention, and archives superseded content under _archive/. Detects drift between docs and disk, flags stale or orphan content, and proposes a reversible cleanup. Hands off to /commit or /ship.

Core Principles

• Plan before act. Write every proposed operation to a plan file and confirm before moving anything.
• Reversible moves only. Archive superseded content; never delete without explicit approval.
• Match disk to docs. Where a project-level docs file exists, treat it as the source of truth and reconcile drift.
• Sync-safe moves. Use shutil.copytree + retry for folder moves on cloud-synced paths (Dropbox, OneDrive, iCloud); never os.rename / mv.
• Conservative by default. Naming, docs, and archiving only. Do not restructure pipelines, scripts, or generated artifacts without explicit scope.
• Hand off, don't chain. End with a clean working tree; /commit or /ship handles commit and push.

Target Structure

These are the structural conventions the skill enforces. They are project-agnostic and can be adapted to any type of work (research, content production, software, data pipelines).

Folder layout

Each project root has a flat top level with these roles, as needed:

Folder	Purpose
data/ or source/	Canonical raw inputs (often gitignored when large)
scripts/	Code or automation
output/ or results/	Generated artifacts (often gitignored when large)
refs/	Reference material, source documents, citations
assets/	Media, images, logos
docs/ or manuscript/	Written deliverables, reports
_archive/	Superseded content at any level (see below)

Not every project needs every folder. Create folders only when at least two items belong there.

Naming rules

Element	Convention	Examples
Folder names (asset / content subfolders)	lowercase, hyphens for word-breaks	refs/, video-captions/, topic-models/
Folder names (nested by identifier)	lowercase, underscores when grouping by id	player_<handle>/, study_01/
Top-level documentation markdown	UPPER_SNAKE_CASE.md	README.md, CHANGELOG.md, CLAUDE.md, VIDEO_SCRIPT.md
Other markdown under folders	kebab-case or lowercase	outline.md, design-notes.md
Scripts	snake_case	run_pipeline.py, generate_report.py
Generated data files	stage/prefix + identifier + optional date	summary_2026-04-14.parquet, batch_001.jsonl
Date tokens in filenames	ISO YYYY-MM-DD or compact YYYYMMDD	snapshot_2026-03-09.xlsx

Root-level folders for distinct projects or subprojects: lowercase kebab-case (video-one/, data-pipeline/).

The _archive/ convention

When a folder produces a superseded version of something (regenerated images, old pipeline output, abandoned drafts), move the old content into a sibling _archive/ folder at the same level it was produced. Do not scatter *_old, *_backup, *_v1 folders around the tree.

• Preserves history without polluting the active workspace
• Date-stamp inside _archive/ when multiple generations accumulate: _archive/2026-04-14/, _archive/v1/
• Archived content stays gitignored only if the originals were; otherwise it remains tracked for historical diffing

Docs-as-anchor

One project-level documentation file (conventionally CLAUDE.md at the repo root) serves as the single source of truth:

• Contains a structure diagram listing every non-ignored top-level folder and the purpose of each
• Documents naming conventions, pipeline order, and any project-specific identifiers
• Is updated whenever folders are added, renamed, or archived

If no such file exists, the skill proposes creating a minimal one.

.gitignore baseline

Every project should ignore at least these categories:

# Secrets
.env
.env.local
*.pem
credentials*.json
token*.json

# Large media (project-specific — adjust)
*.mp3
*.mp4
*.mov

# OS / editor noise
.DS_Store
Thumbs.db
*.swp

# Coding-agent harness state (per-machine)
.claude/settings.local.json
**/.claude/settings.local.json

Specific plugin- or tool-managed directories that live in the project root (non-standard .<tool>/ folders with per-user config) should also be ignored if the tool treats them as per-user. The skill identifies these by the presence of EXTEND.md, settings.local.*, or similar per-user marker files.

Workflow

Step 1: Audit disk vs. docs

Resolve the repo root:

git rev-parse --show-toplevel

If a path argument is provided, scope to that subtree; otherwise scan the whole repo. Enumerate every folder and file under root, skipping .git/, gitignored paths, and any folder already named _archive.

If a project-level docs file exists (CLAUDE.md, README.md), parse any structure diagram it contains and compare against actual disk state.

Step 2: Detect anti-patterns

Run all four detectors and collect findings:

A. Case drift

Compare folder names in the docs structure diagram to disk. On case-insensitive filesystems (Windows, macOS default), disk wins silently. Flag each mismatch.

Default resolution: keep lowercase on disk (Target Structure convention) and update the docs. Only rename folders on disk if the user explicitly asks.

B. Superseded generations next to current

Flag any of these living outside an _archive/ folder:

• Folders named v1/, v2/, ..., old/, backup/, bak/, deprecated/, legacy/
• Siblings with suffix patterns: <name>_v1/, <name>_old/, <name>_backup/, <name>.bak/
• Dated folders sitting next to current content (e.g., 2024-03-09/, MAR09/) with no _archive/ parent

Verify each candidate by diffing contents against the current canonical folder. If the candidate genuinely supersedes current content, propose moving it under a sibling _archive/. Watch for misnamed folders (e.g., a folder named prompts-v1/ whose content actually matches current PNGs in the parent — propose rename to prompts/, not archive).

C. Orphan files

A file is an orphan if no reference to it appears in:

• The project-level docs file (if any)
• Any README.md in the repo
• Any script in the repo (grep for filename and basename across *.py, *.ts, *.r, *.R, *.sh, *.js)
• Any other markdown under the repo (git ls-files '*.md')

Common orphans: ad-hoc PDFs, one-off datasets, test images, manual downloads, screenshots. Propose a destination (refs/, assets/, data/) based on file type, or ask the user for intent. Never delete an orphan without explicit confirmation.

D. Tracked per-machine or per-user state

Check git ls-files for patterns that should be local-only:

• **/.env (allow .env.example through)
• **/.claude/settings.local.json
• Any folder named like .<tool>/ at the repo root whose contents look per-user (marker files such as EXTEND.md, settings.local.*, preferences.json)
• **/.DS_Store, **/Thumbs.db, **/*.swp

For any hits, propose git rm --cached <path> plus the matching .gitignore entry. The file stays on disk — only the index entry is removed.

Step 3: Write plan file

Write all proposed operations to ~/.claude/plans/organize-<repo>-<YYYYMMDD>.md with this structure:

• Context — what triggered this pass, what the repo is, one-sentence goal
• Findings — grouped by the four detectors, each with file paths
• Operations — numbered list of moves, renames, git rm --cached calls, and docs edits
• Out of scope — what was flagged but deliberately not touched, with a reason
• Verification — git status walk, tree walk, cross-check
• Rollback — reverse-move instructions; confirm no destructive ops

Step 4: Clarify ambiguous calls

Use AskUserQuestion for decisions that cannot be inferred:

• Case convention when docs and disk disagree: keep disk + update docs (default), or rename on disk
• Archive vs. delete for superseded content: archive (default), delete only with explicit confirmation
• Destination for orphan files: propose 2-3 existing folders (refs/, assets/, data/); suggest creating a new one only if none fit and user confirms
• Scope: conservative (naming + docs + _archive/) vs. expanded (include pipeline or script reorganization)

Step 5: Apply approved operations

Use a single Python block for all moves, with retries for cloud-sync locks:

import shutil, time
from pathlib import Path

def safe_move(src: Path, dst: Path, retries: int = 5, delay: float = 1.0):
    if not src.exists():
        return
    if dst.exists():
        raise FileExistsError(dst)
    dst.parent.mkdir(parents=True, exist_ok=True)
    for _ in range(retries):
        try:
            shutil.copytree(src, dst) if src.is_dir() else shutil.copy2(src, dst)
            break
        except (PermissionError, OSError):
            time.sleep(delay)
    else:
        raise
    for _ in range(retries):
        try:
            shutil.rmtree(src) if src.is_dir() else src.unlink()
            break
        except (PermissionError, OSError):
            time.sleep(delay)
    else:
        raise

Rules:

• Never os.rename / mv a folder in a cloud-synced path
• Let git detect renames automatically after the move completes; do not git mv
• For tracked harness/plugin state, run git rm --cached <path> (file stays on disk, just untracked)

Step 6: Refresh docs

After operations succeed:

• Update the project-level docs file's structure diagram to match final disk state
• Append convention notes if missing: _archive/ placement rule, subfolder casing rule, gitignored-local-state list
• Update any session-persistent memory files if their path references changed

Step 7: Verify

Run, in order:

git status --short
git ls-files --others --ignored --exclude-standard

Walk the final tree and confirm:

• Every folder named in the docs structure diagram exists on disk
• Every top-level folder on disk is named in the docs (except .git/ and gitignored paths)
• Paths newly gitignored by Detector D no longer appear in git ls-files

Step 8: Hand off

Report a concise structural summary:

• Folders archived / renamed / moved (counts and paths)
• Files untracked via git rm --cached
• Docs edited
• Anything out-of-scope flagged for a follow-up pass

Tell the user: run /commit for a single conventional-commits commit (chore: standardize <repo> structure), or /ship to also update CHANGELOG.md and push.

Scope

Include

• Subfolder casing alignment (docs and disk)
• Archiving superseded generations under _archive/
• Moving orphan files to refs/ / assets/ / data/ (with user confirmation on destination)
• Untracking per-machine or per-user state; extending .gitignore
• Refreshing the project-level docs file (structure diagram and conventions)
• Refreshing session-persistent memory path references

Exclude

• Splitting or merging pipeline, data, or script folders
• Consolidating parallel generation outputs (e.g., two folders holding the same artifacts)
• Deleting files (archive-only unless user explicitly confirms deletion)
• Running /commit or /ship (explicit hand-off)
• Renaming folders across casing conventions on disk (only on explicit request)
• Reorganizing anything inside .git/ or gitignored paths

Checklist

• Audit walked disk and parsed the project-level docs structure diagram
• All four detectors ran (case drift, superseded, orphans, tracked local state)
• Plan file written to ~/.claude/plans/organize-<repo>-<date>.md
• Ambiguous calls resolved via AskUserQuestion, not assumed
• Moves used sync-safe copytree + retry pattern, not rename / mv
• Project-level docs file reflects final disk state
• .gitignore covers any per-machine or per-user state flagged by Detector D
• Hand-off message tells the user to run /commit or /ship