Cleanup & Organization Expert - V3

Purpose

Phase-aware project organization skill that analyzes and maintains clean, well-structured codebases. Understands project conventions, identifies redundancy, consolidates files, and removes obsolete content while respecting your current development phase.

Key Capabilities

• Analyze project state - Understand current folder structure
• Detect redundancy - Find duplicate and overlapping content
• Consolidate files - Merge redundant documentation
• Remove obsolete content - Identify and delete deprecated files
• Phase-appropriate cleanup - Different standards per phase
• Generate reports - Detailed operation logs

When to Invoke

Use this skill when:

• Project has accumulated duplicate/scattered files
• Multiple files contain redundant content
• Files need reorganization
• Obsolete files need removal
• After major refactoring
• Before shipping to next phase

Command: /cleanup or invoke via Skill tool

Phase-Appropriate Cleanup

Prototype Phase

• Minimal cleanup - Keep it loose
• Remove only obvious duplicates
• Don't enforce strict organization
• Focus: Keep it shipping

MVP Phase

• Basic organization - Some structure
• Consolidate major duplicates
• Remove clearly obsolete files
• Focus: Maintain clarity

Growth Phase

• Structured cleanup - Enforce conventions
• Detect and merge redundant docs
• Organize by standards
• Focus: Maintainability

Scale Phase

• Complete organization - Full enforcement
• Comprehensive redundancy detection
• Strict folder structure
• Focus: Enterprise quality

Workflow

1. Analyze Current State

Understand project phase:

# Check current phase
cat .khujta/phase.json

Scan project structure:

• Read project documentation (CLAUDE.md, README.md)
• Identify key folders (ai-state/, docs/, src/, tests/)
• Map current file locations
• Detect patterns and conventions

Generate state report:

• Total files by type/category
• Misplaced files (wrong location)
• Duplicate/redundant content
• Obsolete file candidates
• Phase compliance status

2. Detect Redundancy

Content Similarity Analysis:

• Compare file contents pairwise
• Calculate similarity scores (0-100%)
• Identify duplicate/near-duplicate clusters
• Group files by content similarity

Pattern Recognition:

• Versioned files (file_v1.md, file_v2.md, file_final.md)
• Dated files (notes_2025_10.md, notes_2025_11.md)
• Topic variants (auth.md, authentication.md, login.md)

Redundancy Scoring:

• HIGH (9-10): Immediate consolidation recommended
• MEDIUM (6-8): User review suggested
• LOW (3-5): Optional optimization

Phase-Appropriate Thresholds:

• Prototype: Only flag 95%+ similarity (near-identical)
• MVP: Flag 80%+ similarity
• Growth: Flag 70%+ similarity
• Scale: Flag 60%+ similarity

3. Categorize Files

Decision tree per phase:

FILE → Check phase requirements
       ├─ Prototype → Skip unless obvious duplicate
       ├─ MVP → Basic categorization
       ├─ Growth → Structured organization
       └─ Scale → Strict enforcement

     → Is it redundant?
       ├─ YES → Flag for merge/consolidate
       └─ NO → Is it in correct location?
               ├─ YES → Skip
               └─ NO → Flag for move

     → Is it obsolete?
       ├─ YES → Flag for deletion
       └─ NO → Keep

4. Plan Operations

Group operations by type:

1. MERGE - Consolidate redundant files
2. MOVE - Relocate misplaced files
3. DELETE - Remove obsolete files
4. RENAME - Standardize naming

Phase-Appropriate Planning:

• Prototype: Only merges and deletes
• MVP: Add basic moves
• Growth: Full organization
• Scale: Strict enforcement + renames

Safety checks:

• Verify destinations exist
• Check for overwrite conflicts
• Confirm deletion safety
• Preserve unique content

5. Execute with Approval

Present operation plan:

## Cleanup Plan for [Phase] Phase

**Current State**:
- 156 files total
- 8 redundant files detected
- 5 misplaced files
- 3 obsolete files

**Proposed Operations**:

### MERGE (3 operations)
1. setup_v1.md + setup_v2.md → setup.md
   Similarity: 85% | Recommendation: Keep latest

### MOVE (5 operations)
1. old_spec.md → ai-state/archive/
2. test_results.md → ai-state/regressions/

### DELETE (3 operations)
1. BACKUP_file.md (obsolete, 92 days old)
2. temp_notes.txt (temporary file)

**Approve? (yes/no/skip-deletes)**

Execute approved operations:

• Perform in safe order: MERGE → MOVE → DELETE
• Log each operation with timestamp
• Handle errors gracefully
• Update operations log

6. Generate Report

Create cleanup report:

# Cleanup Report - [Date]

## Summary
- Phase: [prototype/mvp/growth/scale]
- Operations: 11 total (3 merge, 5 move, 3 delete)
- Files reduced: 156 → 148
- Duration: 2 minutes

## Detailed Operations

### Merges (3)
✅ Merged setup_v1.md + setup_v2.md → setup.md
✅ Consolidated auth docs → authentication.md
✅ Merged test results → TEST_RESULTS.md

### Moves (5)
✅ Moved old_spec.md → ai-state/archive/
...

### Deletions (3)
✅ Deleted BACKUP_file.md
...

## Impact
- Clarity: Improved documentation findability
- Maintenance: Fewer files to update
- Storage: 45KB saved

## Recommendations
- Consider archiving files older than 90 days
- Set up automated cleanup hook

Save report: ai-state/cleanup/cleanup_report_YYYYMMDD.md

File Organization Standards

Standard locations for Khujta Sphere V3:

Obsolescence Detection

Files are likely obsolete if:

• Contains "OLD", "BACKUP", "DEPRECATED", "TEMP" in name
• Creation date > 90 days + no modifications
• Duplicates content in primary files
• References outdated architecture
• Not referenced by any other file

Phase-Appropriate Deletion:

• Prototype: Delete only TEMP and BACKUP files
• MVP: Add files >90 days old
• Growth: Add unreferenced files
• Scale: Comprehensive cleanup

Manual review required:

• Configuration files
• Data files (CSVs, JSONs)
• Files > 100 lines
• Files with "IMPORTANT" markers

Safety Guidelines

CRITICAL RULES:

1. ALWAYS get user approval before executing
2. NEVER delete without showing what will be removed
3. ALWAYS preserve unique content during merges
4. ALWAYS generate operation report for audit
5. Respect phase requirements - don't over-organize in prototype

Dry-run mode: Present plan WITHOUT executing (default)

Execution mode: Only after explicit user approval

Example Usage

Prototype Phase Example

User: /cleanup

Response:

## Cleanup Analysis (Prototype Phase)

**Current State**: 45 files
**Phase Policy**: Minimal cleanup only

**Redundancy Detection**:
- 2 obvious duplicates found (98% similarity)
- Keeping relaxed - prototype phase allows disorder

**Proposed Operations**:

MERGE (2 operations):
1. notes.md + notes_copy.md → notes.md (identical)

DELETE (1 operation):
1. TEMP_scratch.txt (temporary file)

**Phase Note**: Skipping organization - you're in prototype mode!
Ship fast, clean later.

Approve? (yes/no)

Scale Phase Example

User: /cleanup

Response:

## Cleanup Analysis (Scale Phase)

**Current State**: 156 files
**Phase Policy**: Comprehensive cleanup + strict organization

**Redundancy Detection**:
HIGH (3 groups): 85% avg similarity
MEDIUM (2 groups): 70% avg similarity

**Organization Issues**:
- 12 files in wrong locations
- 3 files missing standard naming
- 5 files exceed age threshold (>90 days)

**Proposed Operations**:

MERGE (5 operations):
[... detailed list ...]

MOVE (12 operations):
[... relocations to proper folders ...]

RENAME (3 operations):
[... standardize naming ...]

DELETE (5 operations):
[... obsolete files ...]

**Impact**:
156 → 131 files (16% reduction)
Full standards compliance achieved

Approve? (yes/no/skip-deletes/modify)

Integration with V3 Framework

Works with:

• /test-cleanup command (test-specific cleanup)
• operations-logger skill (logs all operations)
• Phase validator hook (respects phase limits)
• Quality gate hook (maintains standards)

Complementary commands:

• /test-cleanup - Clean test files specifically
• /test-phase [phase] - Switch phase before cleanup
• /regression-quick - Verify after cleanup

Escape Hatches

If cleanup is blocking you:

• /skip-cleanup - Defer organization
• /simple-cleanup - Only obvious duplicates
• /prototype-mode - Switch to minimal requirements

Quality Standards

Cleanup operations must meet (phase-appropriate):

Prototype (6.0/10):

• Remove obvious duplicates only
• Don't enforce strict organization
• Preserve flexibility

MVP (7.0/10):

• Basic redundancy consolidation
• Simple folder organization
• Keep it straightforward

Growth (7.5/10):

• Structured organization
• Comprehensive redundancy detection
• Standards enforcement

Scale (8.0/10):

• Full standards compliance
• Complete redundancy elimination
• Enterprise-grade organization

Output Example

# Cleanup Operation Report

**Date**: 2025-11-06T14:30:00Z
**Phase**: MVP
**Duration**: 3 minutes

## Summary
- Files analyzed: 156
- Operations executed: 11
- Files after cleanup: 148
- Reduction: 5.1%

## Operations

### Merged (3)
✅ setup_v1.md + setup_v2.md → setup.md
   Similarity: 85% | Unique content preserved

### Moved (5)
✅ old_spec.md → ai-state/archive/specs/
✅ test_results_20251105.md → ai-state/regressions/

### Deleted (3)
✅ BACKUP_config.md (obsolete backup)
✅ TEMP_notes.txt (temporary, 92 days old)
✅ old_implementation.md (replaced by current version)

## Impact
- ✅ Documentation clarity improved
- ✅ Easier to find authoritative sources
- ✅ Reduced maintenance overhead

## Next Cleanup Suggested
- In 30 days (or after next major refactoring)
- Consider setting up automated cleanup hook

**Status**: ✅ COMPLETE

Version: 3.0.0 Tier: 1-2 (MVP, Growth, Scale) Skill Type: Project Organization & Maintenance Last Updated: 2025-11-06