organize

/organize -- Project Organization Health

Orientation

Use when: Auditing whether source files are in the right architectural layers, detecting loose files and misplaced assets, or configuring directory manifests and cleanup policies for a project.

Don't use when: You want a structural map of code relationships and module dependencies (use /map), you're moving logic between modules (use /refactor), or you need to execute a single organizational task without a health audit (use /marshal).

Commands

Command	Behavior
/organize	Full flow: scan, detect, recommend, configure
/organize --audit	Check current files against the manifest, report violations
/organize --cleanup	Run dynamic directory cleanup based on TTL policy
/organize --show	Display current organization manifest
/organize --unlock	Set locked: false so enforcement is advisory
/organize --lock	Set locked: true so enforcement blocks violations

Protocol

Step 1: CHECK -- Read Existing Configuration

1. Read .claude/harness.json and check for an organization key
2. If organization exists and user ran bare /organize:
   • Display current convention, root count, placement rule count, dynamic dir count
   • Ask: "Your organization manifest is already configured. Want to audit current compliance, adjust the rules, or reconfigure from scratch?"
   • Route based on answer: audit -> Step 6, adjust -> Step 4, reconfigure -> Step 2
3. If organization exists and user ran --audit: Jump to Step 6
4. If organization exists and user ran --cleanup: Jump to Step 7
5. If no organization key: Continue to Step 2

Step 2: SCAN -- Three-Pass Project Analysis

Every scan runs all three passes. A user running /organize gets the full picture.

Do NOT use find or Get-ChildItem -- use the Glob tool and Bash (git ls-files, du, wc) for cross-platform compatibility.

---

Pass 1: Architectural Compliance

1. Use the Glob tool with pattern **/ to discover directories. Filter out: node_modules, .git, .planning, .citadel, .claude, dist, build, __pycache__, .next, target, .venv, venv. Cap at 200 directories. If too large, scan only top 3 levels.
2. Read package.json, Cargo.toml, pyproject.toml, go.mod, or equivalent for stack
3. Read harness.json for language and framework fields
4. Count files per directory to find the "heavy" areas
5. Check for existing convention signals:
   • src/components/, src/hooks/, src/utils/ -> layer-based
   • src/features/auth/, src/features/dashboard/ -> feature-based
   • src/auth/components/, src/auth/hooks/ -> hybrid
   • Flat src/ with no subdirectories -> flat
   • Mixed signals -> custom (needs user input)
6. If an organization manifest exists, check each placement rule against current files. Count compliant vs. violating files.

Record findings:

Detected: {convention}
Confidence: {high|medium|low}
Roots: [{path, purpose, file_count}]
Signals: [{pattern, evidence, convention_match}]
Anomalies: [{path, issue}]

Scoring: architecture_score = compliant_files / total_source_files * 100. If no manifest exists, score is based on how consistently the detected convention is followed.

---

Pass 2: Filesystem Hygiene

1. Loose files in project root. List every file in the project root. Expected root files:

   • Config: package.json, tsconfig*.json, *.config.{js,ts,mjs,cjs}, .eslintrc*, .prettierrc*, babel.config.*, jest.config.*, vite.config.*, next.config.*, rollup.config.*, webpack.config.*, Cargo.toml, pyproject.toml, go.mod, Makefile, Dockerfile, docker-compose*.yml, .env*, .editorconfig, .gitignore, .gitattributes, .npmrc, .nvmrc, .node-version, .tool-versions
   • Docs: README*, LICENSE*, CHANGELOG*, CONTRIBUTING*, CLAUDE.md, QUICKSTART*, CODE_OF_CONDUCT*, SECURITY*
   • CI/lock: *.lock, package-lock.json, yarn.lock, pnpm-lock.yaml, Gemfile.lock, .github/, .husky/
   • Plugin/harness: .claude/, .planning/, .citadel/, hooks/, hooks_src/, skills/, agents/, scripts/
   • Any file listed in .gitignore

   Everything else in root (images, PDFs, ZIPs, random scripts, stray source files) is a finding.

2. Images and assets outside designated directories. Glob for **/*.{png,jpg,jpeg,gif,svg,ico,webp,mp4,mp3,wav,pdf}. Check if they live under a recognized asset directory (assets/, public/, static/, images/, img/, media/, docs/images/, src/assets/). Files outside are findings.

3. Large files (>1 MB). Use git ls-files -z | xargs -0 stat or equivalent to find tracked files over 1 MB. Report each with path and size.

4. Empty directories. Glob for directories, check which contain zero files (excluding .gitkeep). Report as clutter.

5. Stale files in active directories. Files in src/ not modified in 6+ months while siblings are active. Report as "potentially stale" -- advisory only.

6. Duplicate filenames. Scan for files with identical names in different directories. Flag for awareness.

Scoring: Start at 100, deduct:

• -2 per loose non-standard file in project root
• -1 per misplaced asset file
• -3 per large file (>1 MB) tracked in git
• -1 per empty directory
• -0.5 per potentially stale file (capped at -10)
• -0.5 per duplicate filename (capped at -5)

Floor at 0. hygiene_score = max(0, 100 - deductions).

---

Pass 3: Bloat Detection

1. Project size vs. source size.

   • Total tracked size: git ls-files -z | xargs -0 stat (sum sizes)
   • Source code size: same but filtered to .ts, .tsx, .js, .jsx, .py, .rs, .go, .java, .css, .scss, .html, .md
   • Ratio: source_bytes / total_bytes. Healthy = >60%. Below 40% means non-source dominates.

2. Largest files ranked. List top 10 largest tracked files with sizes.

3. Binary files in git. Glob for: *.{png,jpg,jpeg,gif,ico,webp,mp4,mp3,wav,woff,woff2,ttf,eot,zip,tar,gz,jar,dll,so,dylib,exe,bin,dat,db,sqlite,pdf}. Check if each could be gitignored or moved to Git LFS. Report count and total size.

4. Accidentally committed directories. Check if any of these exist as tracked paths: node_modules/, dist/, build/, .next/, target/, __pycache__/, .venv/, venv/, .cache/, .parcel-cache/, .turbo/, coverage/. Any hit is a critical finding.

5. Compressible assets. PNGs over 500 KB, SVGs over 100 KB, any video/audio file.

Scoring: Start at 100, deduct:

• If source ratio <60%: -(60 - ratio)
• -5 per accidentally committed build/dependency directory
• -2 per binary file in git that should be gitignored or in LFS
• -1 per compressible asset (PNG >500KB, SVG >100KB)
• -3 per video/audio file tracked in git

Floor at 0. bloat_score = max(0, 100 - deductions).

---

Composite Score

composite_score = round(
  architecture_score * 0.40 +
  hygiene_score * 0.35 +
  bloat_score * 0.25
)

Always report all four numbers. Never report just the architecture score.

=== Project Health: {project_name} ===

Architecture:  {score}%  -- source file placement, layer boundaries, test colocation
Hygiene:       {score}%  -- loose files, misplaced assets, stale artifacts, empty dirs
Bloat:         {score}%  -- project size ratio, binaries in git, compressible assets
-------------------------------
Overall:       {composite}%

Follow scores with the most actionable findings from each pass. Group by severity (critical first, advisory last). Cap at 10 findings per pass; note "and N more" if truncated.

Step 3: RECOMMEND -- Present Options

Present a tailored recommendation based on confidence level:

If confidence is HIGH: Present the detected convention and its roots. Ask: [Accept], [Adjust], or [Show alternatives].

If confidence is MEDIUM: Present the detected convention with anomaly count and 2-3 alternatives including reorganization cost (number of files to move). Ask: [1/2/3].

If confidence is LOW: Present the four convention options (feature-based, layer-based, hybrid, flat) with a one-line best-for description each, plus [Custom]. Ask: [1/2/3/4/5].

Wait for user response before proceeding.

Step 4: CONFIGURE -- Write the Organization Manifest

4a. Build the roots tree:

For each detected root directory:

{
  "purpose": "short description of what belongs here",
  "children": { ... }  // recursive, only if subdirectories have distinct purposes
}

Only go 2-3 levels deep.

4b. Build placement rules:

Derive placement rules from the detected convention:

Convention	Example Rules
Feature-based	*.test.ts -> colocated with source, *.types.ts -> colocated
Layer-based	*.test.ts -> __tests__/ or tests/, *.types.ts -> types/
Hybrid	*.test.ts -> colocated within feature, *.types.ts -> {feature}/types/
Flat	No placement rules

For each rule:

{
  "glob": "*.test.{ts,tsx}",
  "rule": "colocated",
  "target": null,
  "reason": "Tests live next to the code they test"
}

Rule types:

• colocated -- file must be in the same directory as its source
• sibling-dir -- file must be in target directory adjacent to source
• root-dir -- file must be under target from project root
• within-root -- file must be under one of the declared roots

Ask the user if they want to adjust any rules before writing.

4c. Build dynamic directory entries:

Scan for directories created dynamically by the harness or tools. For each:

{ "path": ".planning/screenshots/", "scope": "session", "cleanup": "empty-on-expire" }

Scopes: session | campaign | task | permanent

Cleanup strategies: empty-on-expire | archive-then-delete | delete | ignore

4d. Set cleanup policy:

Ask the user:

When dynamic directories expire, how should cleanup work?
1. Auto -- Clean up silently on session end
2. Prompt -- Show what would be cleaned and ask first
3. Manual -- Just report stale directories, don't touch them
[1/2/3] (default: 2)

4e. Write to harness.json:

Read-modify-write. Merge the organization key. Do NOT overwrite other keys.

{
  "organization": {
    "convention": "layer",
    "roots": { ... },
    "placement": [ ... ],
    "dynamic": [ ... ],
    "cleanupPolicy": "prompt",
    "locked": false
  }
}

Set locked: false initially. Tell the user they can run /organize --lock once confident.

Step 5: VERIFY -- Confirm the Manifest Works

1. Run a full three-pass audit (Step 6 logic) against the current codebase
2. Report all three scores plus composite
3. If composite < 60%: warn with top issues
4. If architecture > 80% but hygiene or bloat < 60%: call out the drag and note quick wins
5. Tell the user about --lock, --audit, and --cleanup commands

Step 6: AUDIT -- Full Three-Pass Health Check

Run all three passes from Step 2. Output the composite score block first:

=== Project Health: {project_name} ===

Architecture:  {score}%
Hygiene:       {score}%
Bloat:         {score}%
-------------------------------
Overall:       {composite}%

--- Architecture ({N} violations) ---
  {glob pattern} should be {rule}:
    - {violating_path} -> {expected_path}

--- Hygiene ({N} findings) ---
  Loose files in project root:
    - {filename}
  Images outside asset directories:
    - {path} -> should be {target}
  Large files (>1 MB):
    - {path} ({size})
  Empty directories:
    - {path}

--- Bloat ({N} findings) ---
  Source ratio: {ratio}% ({source_size} source / {total_size} total)
  Top 5 largest files:
    1. {path}  ({size})
  Binary files that could be gitignored:
    - {path} (generated/build output)

--- Suggested Actions ---
  [Concrete fixes, quick wins first, larger reorganizations last]

Run quick fixes (move misplaced files, delete empty dirs)? [y/n]

If the user says yes, execute safe fixes (moves, empty dir removal). Never auto-delete files with content -- only move them or flag for manual review.

Step 7: CLEANUP -- Prune Dynamic Directories

Read the dynamic entries from the organization manifest.

For each entry:

1. Check if the directory exists
2. Determine if expired based on scope:
   • session: check .planning/telemetry/ for last session end timestamp. Files older than last session start are stale.
   • campaign: check .planning/campaigns/ for associated campaign status. If completed or parked, contents are stale.
   • task: check if the task ID still exists.
   • permanent: skip
3. Apply the cleanup strategy for expired entries:
   • empty-on-expire: delete contents, keep directory
   • archive-then-delete: move to .planning/archive/{YYYY-MM-DD}/, then empty
   • delete: remove directory and contents (recreate if in PLANNING_DIRS)
   • ignore: report but don't touch

Respect cleanupPolicy: auto executes silently; prompt asks before each category; manual lists stale dirs without modifying.

Output:

=== Cleanup Report ===
Scanned: {N} dynamic directories
Stale: {M} directories ({total_size})

  {path} ({scope}-scoped, {N} files, {size})
    Strategy: {strategy}
    Action: {Cleaned | Would clean | Skipped}

Summary: {N} directories cleaned, {M} archived, {K} skipped

Fringe Cases

• .planning/ does not exist: Run /do setup first to initialize the harness state directory; then re-run.
• No directories found: Skip scan, suggest flat convention.
• Monorepo detected (multiple package.json): Scan each package root separately. Ask if organization should be per-package or repo-wide.
• User changes convention: Warn about number of files to move. Do NOT auto-move without explicit confirmation.
• Conflict with existing rules: If harness.json protectedFiles conflict with placement rules, warn and ask which takes precedence.
• Dynamic dir doesn't exist yet: Keep the entry in the manifest. Don't warn about missing dynamic dirs.
• Archive directory grows large: If .planning/archive/ exceeds 50MB, warn and suggest manual pruning.

Contextual Gates

Disclosure: "Running project health scan. Phase 3 (cleanup) may move files — will confirm scope before executing." Reversibility: amber — may move files or rename directories in cleanup phase; undo with git checkout -- . or git revert Trust gates:

• Any: run scan and view report (Phases 1-2)
• Familiar (5+ sessions): Phase 3 file moves execute autonomously; novices should stop after Phase 2 (report only)

Quality Gates

• All three passes ran -- never skip a pass
• All three scores plus composite reported
• Project directory tree scanned (Step 2 completed or skipped with existing config)
• User presented with options and made a choice (not auto-decided)
• Organization manifest written to harness.json under organization key
• Placement rules are specific (glob + rule + reason, no vague entries)
• Dynamic directory entries have valid scope and cleanup strategy
• User told about --lock, --audit, and --cleanup commands
• No other harness.json keys modified during write

Exit Protocol

---HANDOFF---
- Health: {composite}% (Architecture {arch}%, Hygiene {hyg}%, Bloat {bloat}%)
- Convention: {convention} applied to {project}
- {N} roots, {M} placement rules, {K} dynamic directories configured
- Top findings: {1-2 most impactful issues from hygiene/bloat passes}
- Enforcement: {"advisory (unlocked)" | "blocking (locked)"}
- Reversibility: amber — file moves undoable with `git checkout -- .`; harness.json changes undoable with `git revert`
- Next: Run `/organize --lock` when confident, `/organize --audit` to recheck
---