CODITECT CORE /docs Root Cleanup Plan

CODITECT-CORE /docs Root Cleanup Plan

Created: 2025-11-22 Status: Ready to Execute Scope: Organize 57 markdown files from docs/ root into 9-category subdirectory structure

📊 Current State

Files in docs/ root: 57 markdown files Target: Move to appropriate subdirectories based on content and purpose

📂 Migration Plan by Category

01-getting-started/ (0 files)

No files to move - already organized

02-architecture/ (8 files)

vision/ (1 file)

PLATFORM-EVOLUTION-ROADMAP.md → 02-architecture/vision/

system-design/ (2 files)

AUTONOMOUS-AGENT-SYSTEM-DESIGN.md → 02-architecture/system-design/
MULTI-AGENT-ARCHITECTURE-BEST-PRACTICES.md → 02-architecture/system-design/

licensing/ (1 file)

LICENSING-STRATEGY-PILOT-PHASE.md → 02-architecture/licensing/

integration/ (2 files - CREATE NEW SUBDIRECTORY)

MULTI-LLM-CLI-INTEGRATION.md → 02-architecture/integration/
SLASH-COMMAND-SYSTEM-ANALYSIS.md → 02-architecture/integration/

memory-context/ (2 files - CREATE NEW SUBDIRECTORY)

MEMORY-CONTEXT-architecture.md → 02-architecture/memory-context/
MEMORY-CONTEXT-VALUE-PROPOSITION.md → 02-architecture/memory-context/

03-project-planning/ (14 files)

master-plans/ (2 files already moved, keep these in root - DUPLICATES!)

CODITECT-MASTER-ORCHESTRATION-PLAN.md (DUPLICATE - already in master-plans/)
CODITECT-ROLLOUT-MASTER-PLAN.md (DUPLICATE - already in master-plans/)

submodule-plans/ (1 file - DUPLICATE!)

CODITECT-CLOUD-PLATFORM-project-plan.md (DUPLICATE - already in submodule-plans/)

sprints/ (4 files - CREATE NEW SUBDIRECTORY)

SPRINT-1-MEMORY-CONTEXT-project-plan.md → 03-project-planning/sprints/
SPRINT-1-MEMORY-CONTEXT-tasklist.md → 03-project-planning/sprints/
ORCHESTRATOR-project-plan.md → 03-project-planning/sprints/
EXECUTION-CHECKLIST.md → 03-project-planning/sprints/

documentation-project/ (5 files - CREATE NEW SUBDIRECTORY)

DOCUMENTATION-REORGANIZATION-project-plan.md → 03-project-planning/documentation-project/
DOCUMENTATION-REORGANIZATION-tasklist-with-checkboxes.md → 03-project-planning/documentation-project/
DOCUMENTATION-CATEGORIZATION-FRAMEWORK.md → 03-project-planning/documentation-project/
DOCUMENTATION-INVENTORY.md → 03-project-planning/documentation-project/
DOCUMENTATION-DEPENDENCIES.md → 03-project-planning/documentation-project/

migration-plans/ (2 files - CREATE NEW SUBDIRECTORY)

ROLLOUT-MASTER-DOCS-MIGRATION-ANALYSIS.md → 03-project-planning/migration-plans/
ROOT-CLEANUP-MIGRATION-PLAN.md → 03-project-planning/migration-plans/

summaries/ (1 file - CREATE NEW SUBDIRECTORY)

PROJECT-PLAN-SUMMARY.md → 03-project-planning/summaries/

04-implementation-guides/ (8 files)

workflows/ (2 files)

EXPORT-AUTOMATION.md → 04-implementation-guides/workflows/
CHECKPOINT-PROCESS-STANDARD.md → 04-implementation-guides/workflows/

standards/ (3 files)

CODITECT-COMPONENT-CREATION-STANDARDS.md → 04-implementation-guides/standards/
CODITECT-STANDARDS-VERIFIED.md → 04-implementation-guides/standards/
NEW-PROJECT-STRUCTURE-WORKFLOW-ANALYSIS.md → 04-implementation-guides/standards/

hooks/ (1 file - CREATE NEW SUBDIRECTORY)

HOOKS-COMPREHENSIVE-ANALYSIS.md → 04-implementation-guides/hooks/

privacy/ (1 file - CREATE NEW SUBDIRECTORY)

PRIVACY-CONTROL-MANAGER.md → 04-implementation-guides/privacy/

processes/ (1 file - DUPLICATE!)

SUBMODULE-UPDATE-PROCESS.md (DUPLICATE - already in 09-special-topics/submodule-management/)

multi-agent-reference/ (1 file)

slash-commands/ (1 file - CREATE NEW SUBDIRECTORY)

SLASH-COMMANDS-REFERENCE.md → multi-agent-reference/slash-commands/

06-research-analysis/ (7 files)

gap-analysis/ (1 file)

CODITECT-GAP-ANALYSIS-REPORT.md → 06-research-analysis/gap-analysis/

code-reviews/ (1 file)

CODE-REVIEW-DAY5.md → 06-research-analysis/code-reviews/

completion-reports/ (3 files)

DAY-1-COMPLETION-REPORT.md → 06-research-analysis/completion-reports/
DOCUMENTATION-DUPLICATES-AND-STALE.md → 06-research-analysis/completion-reports/
TEST-COVERAGE-SUMMARY.md → 06-research-analysis/completion-reports/

performance/ (1 file)

PERFORMANCE-OPTIMIZATIONS-SUMMARY.md → 06-research-analysis/performance/

timelines/ (1 file - CREATE NEW SUBDIRECTORY)

PROJECT-TIMELINE.md (check if DUPLICATE with 03-project-planning/PROJECT-TIMELINE.md)

07-automation-integration/ (0 files)

Already organized

08-training-certification/ (0 files)

Already organized

09-special-topics/ (0 files moved - already in subdirectories)

🔍 Duplicate Files to Remove

These files appear to be duplicates (need verification):

CODITECT-MASTER-ORCHESTRATION-PLAN.md (root) vs 03-project-planning/master-plans/
CODITECT-ROLLOUT-MASTER-PLAN.md (root) vs 03-project-planning/master-plans/
CODITECT-CLOUD-PLATFORM-project-plan.md (root) vs 03-project-planning/submodule-plans/
SUBMODULE-UPDATE-PROCESS.md (root) vs 09-special-topics/submodule-management/
PROJECT-TIMELINE.md (root) vs 03-project-planning/PROJECT-TIMELINE.md

Action: Compare file sizes and checksums, keep newer version, delete duplicate

📋 New Subdirectories to Create

02-architecture/integration/
02-architecture/memory-context/
03-project-planning/sprints/
03-project-planning/documentation-project/
03-project-planning/migration-plans/
03-project-planning/summaries/
04-implementation-guides/hooks/
04-implementation-guides/privacy/
multi-agent-reference/slash-commands/
06-research-analysis/timelines/

✅ Execution Steps

Verify duplicates - Compare file sizes/checksums
Create new subdirectories (10 directories)
Move files with git mv (preserve history)
Remove confirmed duplicates
Update cross-references in key files
Commit changes with detailed message

📊 Summary

Total files to process: 57 Files to move: ~50 (after removing duplicates) Duplicates to verify/remove: 5 New subdirectories: 10 Target: 0 files in docs/ root (except README.md and Claude.md if needed)

Next Action: Execute migration plan systematically by category

ROLLOUT-MASTER DOCS MIGRATION ANALYSIS

Date: November 22, 2025 Objective: Centralize ALL core CODITECT documentation in CODITECT-core/docs/ Principle: CODITECT-core is the BRAIN - agents need ONE location for all framework documentation

📊 Analysis Summary

Total Files in rollout-master/docs/: 93 markdown files

Migration Decision

MOVE to CODITECT-core/docs/: 75 files (81%) - Core framework documentation
KEEP in rollout-master/docs/: 18 files (19%) - Rollout-specific project management only

Rationale: Only rollout-master-specific project management docs stay. Everything else centralizes in CODITECT-core.

✅ MOVE to CODITECT-core/docs/ (75 files)

Category 01: Getting Started (1 file)

QUICKSTART-GUIDE-FOR-NEW-CUSTOMERS.md (12K)
- Target: docs/01-getting-started/
- Reason: New user onboarding - core framework documentation

Category 02: Architecture (35 files)

Vision & Strategy (3 files)

AZ1.AI-CODITECT-VISION-AND-STRATEGY.md (20K)

Target: docs/02-architecture/vision/
Reason: Core CODITECT vision - framework architecture

CODITECT-INTEGRATED-ECOSYSTEM-VISION.md (23K)
- Target: docs/02-architecture/vision/
- Reason: Ecosystem architecture vision
CODITECT-BUILDS-CODITECT.md (20K)
- Target: docs/02-architecture/vision/
- Reason: Meta-concept of self-building framework

Architecture Documents (10 files)

CODITECT-C4-ARCHITECTURE-EVOLUTION.md (50K)

Target: docs/02-architecture/c4-diagrams/
Reason: Core C4 architecture methodology

C4-DIAGRAMS-PROJECT-INTELLIGENCE.md (43K)
- Target: docs/02-architecture/c4-diagrams/
- Reason: C4 diagrams for project intelligence module
CODITECT-ECOSYSTEM-INTEGRATION-MAP.md (28K)
- Target: docs/02-architecture/integration/
- Reason: Framework integration architecture
CODITECT-REUSABLE-TOOLS-architecture.md (33K)
- Target: docs/02-architecture/tools/
- Reason: Reusable tools architecture patterns
CODITECT-SHARED-DATA-MODEL.md (25K)
- Target: docs/02-architecture/data-models/
- Reason: Core shared data model across framework
DATABASE-ARCHITECTURE-PROJECT-INTELLIGENCE.md (29K)
- Target: docs/02-architecture/database/
- Reason: Database architecture for framework modules
SOFTWARE-DESIGN-DOCUMENT-PROJECT-INTELLIGENCE.md (63K)
- Target: docs/02-architecture/software-design/
- Reason: Comprehensive software design document
DISTRIBUTED-INTELLIGENCE-COMPLETE.md (3.2K)
- Target: docs/02-architecture/distributed-intelligence/
- Reason: Distributed intelligence completion summary
DISTRIBUTED-INTELLIGENCE-VERIFICATION.md (3.5K)
- Target: docs/02-architecture/distributed-intelligence/
- Reason: Distributed architecture verification
INFRASTRUCTURE-ANALYSIS-GKE-INTEGRATION-VS-SEPARATION.md (16K)
- Target: docs/02-architecture/infrastructure/
- Reason: Infrastructure architecture analysis

ADRs - Architecture Decision Records (10 files)

adrs/project-intelligence/ADR-001-git-as-source-of-truth.md
adrs/project-intelligence/ADR-002-PostgreSQL-as-primary-database.md
adrs/project-intelligence/ADR-003-chromadb-for-semantic-search.md
adrs/project-intelligence/ADR-004-multi-tenant-strategy.md
adrs/project-intelligence/ADR-005-fastapi-over-flask-django.md
adrs/project-intelligence/ADR-006-react-nextjs-frontend.md
adrs/project-intelligence/ADR-007-gcp-cloud-run-deployment.md
adrs/project-intelligence/ADR-008-role-based-access-control.md
adrs/project-intelligence/ADR-COMPLIANCE-REPORT.md
adrs/project-intelligence/README.md
- Target: docs/02-architecture/adrs/
- Reason: Architecture decisions are core framework documentation

TOON Architecture (12 files)

TOON-ARCHITECTURE-REVIEW-EXECUTIVE-SUMMARY.md (13K)
TOON-ARCHITECTURE-REVIEW.md (32K)
TOON-BEST-PRACTICES-COMPLIANCE-REPORT.md (78K)
TOON-COMPREHENSIVE-CODE-REVIEW-REPORT.md (32K)
TOON-DUAL-FORMAT-STRATEGY.md (23K)
TOON-FORMAT-INTEGRATION-ANALYSIS.md (29K)
TOON-MODULE-TECHNICAL-SPECIFICATION.md (26K)
TOON-PERFORMANCE-ANALYSIS-AND-SCALABILITY-ASSESSMENT.md (38K)
TOON-PERFORMANCE-METRICS-DASHBOARD.md (33K)
TOON-TEST-PYRAMID-VISUALIZATION.md (26K)
TOON-TESTING-EXECUTIVE-SUMMARY.md (21K)
TOON-TESTING-STRATEGY-AND-IMPLEMENTATION.md (70K)
- Target: docs/02-architecture/toon-integration/
- Reason: TOON is a framework component, all arch/testing docs are core

Category 03: Project Planning (6 files)

Core Project Plans (moved from rollout to framework)

CODITECT-CLOUD-PLATFORM-project-plan.md (20K)
- Target: docs/03-project-planning/cloud-platform/
- Reason: Cloud platform is a framework component plan
MASTER-ORCHESTRATION-FRAMEWORK.md (38K)
- Target: docs/03-project-planning/orchestration/
- Reason: Orchestration framework concepts (not rollout-specific)
TOON-INTEGRATION-project-plan.md (18K)
TOON-INTEGRATION-SUMMARY.md (16K)
TOON-INTEGRATION-tasklist.md (25K)
- Target: docs/03-project-planning/toon-integration/
- Reason: TOON integration planning is framework-level
2025-11-17-strategic-development-plan.md (38K)
- Target: docs/03-project-planning/strategic/
- Reason: Strategic framework development plan

Category 04: Implementation Guides (11 files)

CODITECT-CODE-SAFETY-SYSTEM.md (31K)
- Target: docs/04-implementation-guides/safety/
- Reason: Code safety patterns - core implementation guide
AUTOMATED-CHECKPOINT-WORKFLOW.md (14K)
- Target: docs/04-implementation-guides/processes/
- Reason: Checkpoint workflow is a core process
CODITECT-COMPREHENSIVE-CHECKPOINT-SYSTEM.md (37K)
- Target: docs/04-implementation-guides/processes/
- Reason: Comprehensive checkpoint system guide
DEDUPLICATION-RESEARCH-REVIEW-GUIDE.md (18K)
- Target: docs/04-implementation-guides/processes/
- Reason: Deduplication process guide
FILE-ORGANIZATION-GUIDE.md (7.5K)
- Target: docs/04-implementation-guides/organization/
- Reason: File organization standards for all CODITECT projects
README-AUTOMATED-WORKFLOW.md (6.6K)
- Target: docs/04-implementation-guides/automation/
- Reason: README automation workflow
README-TEMPLATE-STANDARD.md (7.1K)
- Target: docs/04-implementation-guides/standards/
- Reason: README template standards for all projects
REPO-NAMING-CONVENTION.md (6.5K)
- Target: docs/04-implementation-guides/standards/
- Reason: Repository naming standards for framework
SUBMODULE-CREATION-QUICK-REFERENCE.md (8.8K)
- Target: docs/04-implementation-guides/submodules/
- Reason: Submodule creation is a framework capability
SUBMODULE-UPDATE-PROCESS.md (3.8K)
- Target: docs/04-implementation-guides/submodules/
- Reason: Submodule update process - framework guide
CODITECT-LICENSE-MANAGEMENT-STRATEGY.md (48K)
- Target: docs/04-implementation-guides/licensing/
- Reason: License management is a framework component

Category 05: Agent Reference (1 file)

EXECUTIVE-SUMMARY-PROJECT-INTELLIGENCE.md (15K)
- Target: docs/multi-agent-reference/
- Reason: Project intelligence module reference

Category 06: Research & Analysis (6 files)

DOCUMENTATION-ASSESSMENT-SUMMARY.md (13K)
- Target: docs/06-research-analysis/documentation/
- Reason: Documentation quality analysis
TOON-DOCUMENTATION-GAPS-ACTION-PLAN.md (12K)
TOON-DOCUMENTATION-QUALITY-ASSESSMENT.md (45K)
- Target: docs/06-research-analysis/documentation/
- Reason: Documentation analysis and gaps
PERFORMANCE-ANALYSIS-EXECUTIVE-SUMMARY.md (15K)
PERFORMANCE-OPTIMIZATION-QUICK-REFERENCE.md (11K)
- Target: docs/06-research-analysis/performance/
- Reason: Performance analysis research
SESSION-SUMMARY-2025-11-17-PROJECT-INTELLIGENCE.md (13K)
- Target: docs/06-research-analysis/session-summaries/
- Reason: Research session summary

Category 09: Special Topics (15 files)

Memory Context & Deduplication (11 files)

Claude-SESSION-MEMORY-EXTRACTION-STRATEGY.md (19K)
Claude-SESSION-MEMORY-INVESTIGATION.md (13K)
MEMORY-CONTEXT-architecture-analysis.md (57K)
MEMORY-CONTEXT-DAY1-DELIVERABLES.md (16K)
MEMORY-CONTEXT-RECOMMENDATION-SUMMARY.md (9.2K)
MEMORY-CONTEXT-WEEK1-IMPLEMENTATION.md (13K)
- Target: docs/09-special-topics/memory-context/
- Reason: Memory context system is a framework component
CONVERSATION-DEDUPLICATION-architecture.md (54K)
CONVERSATION-DEDUPLICATION-DATABASE-DESIGN.md (46K)
CONVERSATION-DEDUPLICATION-IMPLEMENTATION-PLAN.md (28K)
EXPORT-DEDUP-METRICS-DISPLAY.md (7.4K)
EXPORT-DEDUP-STATUS-REPORTS.md (11K)
- Target: docs/09-special-topics/memory-context/deduplication/
- Reason: Deduplication is part of memory context system

Submodule Management Framework (4 files)

SUBMODULE-ANALYSIS-FRAMEWORK.md (22K)
- Target: docs/09-special-topics/submodule-management/
- Reason: Submodule analysis framework - reusable capability
SUBMODULE-CREATION-VERIFICATION-SUMMARY.md (11K)
- Target: docs/09-special-topics/submodule-management/
- Reason: Submodule verification - framework process
SYMLINKS-STATUS.md (2.1K)
- Target: docs/09-special-topics/distributed-intelligence/
- Reason: Symlink status for distributed intelligence
WEEK-1-ORCHESTRATION-PLAN.md (878B)
- Target: docs/09-special-topics/planning/
- Reason: Generic orchestration planning template

⏸️ KEEP in rollout-master/docs/ (18 files)

CLEAR JUSTIFICATION REQUIRED: These files are SPECIFIC to managing the CODITECT-rollout-master repository and its 42 submodules rollout project.

Rollout Project Plans (6 files)

CODITECT-ROLLOUT-MASTER-PLAN.md (18K)
- Reason: Specific plan for rolling out the 42-submodule master repository
- Scope: CODITECT-rollout-master repo management
CODITECT-MASTER-ORCHESTRATION-PLAN.md (42K)
- Reason: Plan for orchestrating the rollout-master repository structure
- Scope: Master repo submodule coordination
PROJECT-PLAN-REPO-REORGANIZATION.md (13K)
- Reason: Plan specific to reorganizing rollout-master repository
- Scope: Rollout-master restructuring
PROJECT-PLAN-README-STANDARDIZATION.md (12K)
- Reason: Plan for standardizing READMEs across 42 submodules in rollout
- Scope: Rollout-master submodule management task
PROJECT-PLAN-SKILLS-STANDARDIZATION.md (9.8K)
- Reason: Plan for standardizing skills across rollout submodules
- Scope: Rollout-master specific standardization
PROJECT-PLAN-UPDATE-2025-11-16-ARCHITECTURE-SPRINT.md (17K)
- Reason: Sprint update specific to rollout-master project
- Scope: Rollout project sprint status

Rollout Timelines (2 files)

PROJECT-TIMELINE.md (13K)
- Reason: Timeline for rolling out the 42-submodule master repository
- Scope: Rollout project schedule
PROJECT-TIMELINE-ENHANCED.md (14K)
- Reason: Enhanced timeline for rollout project
- Scope: Rollout project schedule

Rollout Task Lists (4 files)

TASKLIST-Claude-MD-CREATION.md (6.4K)
- Reason: Tasklist for creating Claude.md in all 42 submodules
- Scope: Rollout-master specific task
TASKLIST-README-STANDARDIZATION.md (13K)
- Reason: Tasklist for README standardization across submodules
- Scope: Rollout-master specific task
TASKLIST-REPO-REORGANIZATION.md (18K)
- Reason: Tasklist for reorganizing rollout-master repository
- Scope: Rollout-master restructuring task
TASKLIST-SKILLS-STANDARDIZATION.md (22K)
- Reason: Tasklist for skills standardization across submodules
- Scope: Rollout-master specific task

Rollout Status & Audits (4 files)

REPOSITORY-AUDIT-2025-11-19.md (12K)
- Reason: Audit of rollout-master repository state
- Scope: Rollout-master status snapshot
ROLLOUT-RESTRUCTURE-PROPOSAL-v1.md (12K)
- Reason: Proposal for restructuring rollout-master
- Scope: Rollout-master architecture proposal
DOCUMENTATION-IMPROVEMENT-CHECKLIST.md (27K)
- Reason: Checklist for improving rollout-master documentation
- Scope: Rollout-master documentation task
project-management/FINAL-ROOT-CLEANUP-REPORT.md
- Reason: Report on cleaning up rollout-master root directory
- Scope: Rollout-master cleanup status

Rollout Submodule Migration (2 files)

SUBMODULE-MIGRATION-PLAN.md (14K)
- Reason: Plan for migrating submodules to rollout-master structure
- Scope: Rollout-master submodule migration
SUBMODULE-MIGRATION-PLAN-UPDATED.md (16K)
- Reason: Updated migration plan for rollout submodules
- Scope: Rollout-master submodule migration

Rollout README

project-management/REORGANIZATION-SUMMARY.md
- Reason: Summary of rollout-master reorganization
- Scope: Rollout-master project status
README.md (37K)
- Reason: Index for rollout-master/docs directory
- Scope: Rollout-master docs navigation

📋 Migration Execution Plan

Phase 1: Create Target Directories in CODITECT-core/docs/

cd /Users/halcasteel/PROJECTS/coditect-rollout-master/submodules/core/coditect-core/docs

# Category 02: Architecture subdirectories
mkdir -p 02-architecture/vision
mkdir -p 02-architecture/c4-diagrams
mkdir -p 02-architecture/integration
mkdir -p 02-architecture/tools
mkdir -p 02-architecture/data-models
mkdir -p 02-architecture/database
mkdir -p 02-architecture/software-design
mkdir -p 02-architecture/infrastructure
mkdir -p 02-architecture/adrs
mkdir -p 02-architecture/toon-integration

# Category 03: Project Planning subdirectories
mkdir -p 03-project-planning/cloud-platform
mkdir -p 03-project-planning/orchestration
mkdir -p 03-project-planning/toon-integration
mkdir -p 03-project-planning/strategic

# Category 04: Implementation Guides subdirectories
mkdir -p 04-implementation-guides/safety
mkdir -p 04-implementation-guides/processes
mkdir -p 04-implementation-guides/organization
mkdir -p 04-implementation-guides/automation
mkdir -p 04-implementation-guides/submodules
mkdir -p 04-implementation-guides/licensing

# Category 06: Research & Analysis subdirectories
mkdir -p 06-research-analysis/documentation
mkdir -p 06-research-analysis/session-summaries

# Category 09: Special Topics subdirectories
mkdir -p 09-special-topics/memory-context/deduplication
mkdir -p 09-special-topics/submodule-management
mkdir -p 09-special-topics/planning

Phase 2: Move Files (75 git mv commands)

Due to length, migration script will be in separate file

Phase 3: Update Cross-References

Update README.md in both repos
Update Claude.md references
Update internal doc links
Validate all links

Create README.md and Claude.md in each new subdirectory:

02-architecture/ (10 subdirectories)
03-project-planning/ (4 subdirectories)
04-implementation-guides/ (6 subdirectories)
06-research-analysis/ (2 subdirectories)
09-special-topics/ (3 subdirectories)

📊 Impact Summary

Before

rollout-master/docs/: 93 files
CODITECT-core/docs/: 38 files (after today's root cleanup)
Total: 131 files across 2 locations

After

rollout-master/docs/: 18 files (rollout-specific only)
CODITECT-core/docs/: 113 files (centralized brain)
Total: 131 files (same total, better organized)

Benefits

✅ ONE central location for all CODITECT framework documentation
✅ Agents know where to look (CODITECT-core/docs/)
✅ Clear separation: rollout-master = project management, CODITECT-core = framework
✅ Easier to maintain single source of truth
✅ Better for documentation versioning

Rollout-master becomes

Master orchestration repository for 42 submodules
Contains ONLY rollout project management docs
Points to CODITECT-core for all framework documentation

✅ Validation Checklist

All 75 files categorized with clear target locations
18 files staying in rollout-master have clear justification
Migration script created with git mv commands
Cross-reference update plan created
Navigation README.md/Claude.md plan created
No duplicates between repos
Single source of truth established

Status: Analysis Complete - Ready for Approval Files to Move: 75 (81%) Files to Keep: 18 (19% - rollout-specific only) Next Step: Execute migration with git mv

ROOT DIRECTORY CLEANUP - FINAL MIGRATION PLAN

Date: November 22, 2025 Objective: Clean root directory to production-ready state with ONLY 2 essential files Status: Ready for execution

🎯 Executive Summary

Target State: Root directory contains ONLY 2 files:

README.md - Primary repository documentation
Claude.md - AI agent configuration

Files to Move: ALL 19 other markdown files → docs/ subdirectories

Impact

Root reduction: 21 files → 2 files (90% cleanup)
All files properly categorized in docs/
Cross-references updated (80-120 links)
Git history preserved via git mv

📋 Complete Migration Plan (19 Files)

Category 01: Getting Started (4 files)

1-2-3-SLASH-COMMAND-quick-start.md (16K)
- Target: docs/01-getting-started/quick-starts/
AZ1.AI-CODITECT-1-2-3-QUICKSTART.md (28K)
- Target: docs/01-getting-started/quick-starts/
DEVELOPMENT-SETUP.md (13K)
- Target: docs/01-getting-started/installation/
SHELL-SETUP-GUIDE.md (8.7K)
- Target: docs/01-getting-started/configuration/

Category 02: Architecture (2 files)

C4-ARCHITECTURE-METHODOLOGY.md (17K)
- Target: docs/02-architecture/system-design/
WHAT-IS-CODITECT.md (26K)
- Target: docs/02-architecture/distributed-intelligence/

Category 03: Project Planning (3 files) ⭐ UPDATED

project-plan.md (70K)
- Previous: Keep at root
- NEW TARGET: docs/03-project-planning/
- Rationale: Clean root, easily accessible from docs/
tasklist-with-checkboxes.md (49K)
- Previous: Keep at root
- NEW TARGET: docs/03-project-planning/
- Rationale: Belongs with project planning materials
CHECKPOINT-2025-11-22-DOCUMENTATION-REORGANIZATION-PHASE-0-COMPLETE.md (21K)
- Target: docs/03-project-planning/checkpoints/

Category 04: Implementation Guides (2 files)

CODITECT-ARCHITECTURE-STANDARDS.md (49K)
- Target: docs/04-implementation-guides/standards/
STANDARDS.md (10K)
- Target: docs/04-implementation-guides/standards/

Category 05: Agent Reference (2 files) ⭐ UPDATED

AGENT-INDEX.md (10K)
- Previous: Keep at root
- NEW TARGET: docs/multi-agent-reference/
- Rationale: Index of agents, belongs in reference section
COMPLETE-INVENTORY.md (24K)
- Target: docs/multi-agent-reference/

Category 06: Research & Analysis (4 files)

COMPONENT-CONFORMANCE-ANALYSIS.md (8.5K)
- Target: docs/06-research-analysis/code-reviews/
SCRIPT-IMPROVEMENTS.md (17K)
- Target: docs/06-research-analysis/completion-reports/
SUBMODULE-CREATION-AUTOMATION-AUDIT.md (24K)
- Target: docs/06-research-analysis/gap-analysis/
VERIFICATION-REPORT.md (13K)
- Target: docs/06-research-analysis/completion-reports/

Category 09: Special Topics (2 files)

MEMORY-CONTEXT-GUIDE.md (11K)
- Target: docs/09-special-topics/memory-context/
README-EDUCATIONAL-FRAMEWORK.md (9.1K)
- Target: docs/09-special-topics/legacy/

🚀 Migration Script (Updated)

#!/bin/bash
# ROOT CLEANUP - Move ALL files except README.md and CLAUDE.md
# Preserves git history using git mv

set -e

echo "🎯 GOAL: Root directory with ONLY README.md and CLAUDE.md"
echo ""
echo "📁 Creating target directory structure..."

# Create all required subdirectories
mkdir -p docs/01-getting-started/installation
mkdir -p docs/01-getting-started/quick-starts
mkdir -p docs/01-getting-started/configuration
mkdir -p docs/02-architecture/system-design
mkdir -p docs/02-architecture/distributed-intelligence
mkdir -p docs/03-project-planning/checkpoints
mkdir -p docs/04-implementation-guides/standards
mkdir -p docs/multi-agent-reference
mkdir -p docs/06-research-analysis/code-reviews
mkdir -p docs/06-research-analysis/completion-reports
mkdir -p docs/06-research-analysis/gap-analysis
mkdir -p docs/09-special-topics/memory-context
mkdir -p docs/09-special-topics/legacy

echo "✅ Directory structure created"
echo ""
echo "🚚 Migrating ALL files except README.md and CLAUDE.md..."

# Category 01: Getting Started (4 files)
echo "  → Getting Started (4 files)..."
git mv 1-2-3-SLASH-COMMAND-quick-start.md docs/01-getting-started/quick-starts/
git mv AZ1.AI-CODITECT-1-2-3-QUICKSTART.md docs/01-getting-started/quick-starts/
git mv DEVELOPMENT-SETUP.md docs/01-getting-started/installation/
git mv SHELL-SETUP-GUIDE.md docs/01-getting-started/configuration/

# Category 02: Architecture (2 files)
echo "  → Architecture (2 files)..."
git mv C4-ARCHITECTURE-METHODOLOGY.md docs/02-architecture/system-design/
git mv WHAT-IS-CODITECT.md docs/02-architecture/distributed-intelligence/

# Category 03: Project Planning (3 files) - NOW INCLUDING PROJECT-PLAN AND TASKLIST
echo "  → Project Planning (3 files) - including project-plan.md and TASKLIST..."
git mv project-plan.md docs/03-project-planning/
git mv tasklist-with-checkboxes.md docs/03-project-planning/
if [ -f "CHECKPOINT-2025-11-22-DOCUMENTATION-REORGANIZATION-PHASE-0-COMPLETE.md" ]; then
  git mv CHECKPOINT-2025-11-22-DOCUMENTATION-REORGANIZATION-PHASE-0-COMPLETE.md docs/03-project-planning/checkpoints/
fi

# Category 04: Implementation Guides (2 files)
echo "  → Implementation Guides (2 files)..."
git mv CODITECT-ARCHITECTURE-STANDARDS.md docs/04-implementation-guides/standards/
git mv STANDARDS.md docs/04-implementation-guides/standards/

# Category 05: Agent Reference (2 files) - NOW INCLUDING AGENT-INDEX
echo "  → Agent Reference (2 files) - including AGENT-INDEX.md..."
git mv AGENT-INDEX.md docs/multi-agent-reference/
git mv COMPLETE-INVENTORY.md docs/multi-agent-reference/

# Category 06: Research & Analysis (4 files)
echo "  → Research & Analysis (4 files)..."
git mv COMPONENT-CONFORMANCE-ANALYSIS.md docs/06-research-analysis/code-reviews/
git mv SCRIPT-IMPROVEMENTS.md docs/06-research-analysis/completion-reports/
git mv SUBMODULE-CREATION-AUTOMATION-AUDIT.md docs/06-research-analysis/gap-analysis/
git mv VERIFICATION-REPORT.md docs/06-research-analysis/completion-reports/

# Category 09: Special Topics (2 files)
echo "  → Special Topics (2 files)..."
git mv MEMORY-CONTEXT-GUIDE.md docs/09-special-topics/memory-context/
git mv README-EDUCATIONAL-FRAMEWORK.md docs/09-special-topics/legacy/

echo ""
echo "✅ Migration complete!"
echo ""
echo "📋 Root directory status:"
ls -1 *.md 2>/dev/null | tee /tmp/root_md_files.txt
echo ""
ROOT_COUNT=$(ls -1 *.md 2>/dev/null | wc -l | xargs)
echo "📊 Markdown files at root: $ROOT_COUNT"
echo "🎯 Target: 2 files (README.md, CLAUDE.md)"

if [ "$ROOT_COUNT" -eq 2 ]; then
  echo "✅ SUCCESS: Root is production-ready!"
else
  echo "⚠️  WARNING: Expected 2 files, found $ROOT_COUNT"
  echo "   Files at root:"
  cat /tmp/root_md_files.txt
fi

echo ""
echo "⚠️  NEXT STEP: Run link update script to fix cross-references"

🔗 Updated Cross-Reference Script

#!/bin/bash
# Cross-Reference Update Script
# Updates links after moving ALL files except README.md and CLAUDE.md

set -e

echo "🔗 Updating cross-references..."

# ===== README.md updates (stays at root) =====
echo "  → README.md (stays at root, links to moved files)..."

# Previously root-level files now in docs/
sed -i.bak 's|\[WHAT-IS-CODITECT\.md\](#)|[WHAT-IS-CODITECT.md](#)|g' README.md

sed -i.bak 's|\[AZ1\.AI-CODITECT-1-2-3-QUICKSTART\.md\](#)|[AZ1.AI-CODITECT-1-2-3-QUICKSTART.md](#)|g' README.md

sed -i.bak 's|\[1-2-3-SLASH-COMMAND-QUICK-START\.md\](#)|[1-2-3-SLASH-COMMAND-quick-start.md](#)|g' README.md

sed -i.bak 's|\[C4-ARCHITECTURE-METHODOLOGY\.md\](#)|[C4-ARCHITECTURE-METHODOLOGY.md](#)|g' README.md

sed -i.bak 's|\[README-EDUCATIONAL-FRAMEWORK\.md\](#)|[README-EDUCATIONAL-FRAMEWORK.md](#)|g' README.md

sed -i.bak 's|\[DEVELOPMENT-SETUP\.md\](#)|[DEVELOPMENT-SETUP.md](#)|g' README.md

sed -i.bak 's|\[SHELL-SETUP-GUIDE\.md\](#)|[SHELL-SETUP-GUIDE.md](#)|g' README.md

sed -i.bak 's|\[MEMORY-CONTEXT-GUIDE\.md\](#)|[MEMORY-CONTEXT-GUIDE.md](#)|g' README.md

sed -i.bak 's|\[COMPLETE-INVENTORY\.md\](#)|[COMPLETE-INVENTORY.md](#)|g' README.md

sed -i.bak 's|\[CODITECT-ARCHITECTURE-STANDARDS\.md\](#)|[CODITECT-ARCHITECTURE-STANDARDS.md](#)|g' README.md

# NEW: Update AGENT-INDEX.md reference
sed -i.bak 's|\[AGENT-INDEX\.md\](#)|[AGENT-INDEX.md](#)|g' README.md

# NEW: Update project-plan.md and TASKLIST references
sed -i.bak 's|\[PROJECT-PLAN\.md\](#)|[project-plan.md](#)|g' README.md

sed -i.bak 's|\[TASKLIST-WITH-CHECKBOXES\.md\](#)|[tasklist-with-checkboxes.md](#)|g' README.md

echo "✅ README.md updated"

# ===== CLAUDE.md updates (stays at root) =====
echo "  → CLAUDE.md (stays at root, training material references)..."

# Update project-plan.md reference if it exists
sed -i.bak 's|\[PROJECT-PLAN\.md\](#)|[project-plan.md](#)|g' CLAUDE.md

# Update TASKLIST reference if it exists
sed -i.bak 's|\[TASKLIST-WITH-CHECKBOXES\.md\](#)|[tasklist-with-checkboxes.md](#)|g' CLAUDE.md

# Update AGENT-INDEX reference if it exists
sed -i.bak 's|\[AGENT-INDEX\.md\](#)|[AGENT-INDEX.md](#)|g' CLAUDE.md

echo "✅ CLAUDE.md updated"

# ===== SHELL-SETUP-GUIDE.md updates (now in docs/) =====
echo "  → SHELL-SETUP-GUIDE.md (now in docs/01-getting-started/configuration/)..."

cd docs/01-getting-started/configuration/

sed -i.bak 's|\[1-2-3-SLASH-COMMAND-QUICK-START\.md\](#)|[1-2-3-SLASH-COMMAND-quick-start.md](#)|g' SHELL-SETUP-GUIDE.md

sed -i.bak 's|\[docs/SLASH-COMMANDS-REFERENCE\.md\](#)|[SLASH-COMMANDS-REFERENCE.md](#)|g' SHELL-SETUP-GUIDE.md

sed -i.bak 's|\[scripts/README\.md\](#)|[scripts/README.md](#)|g' SHELL-SETUP-GUIDE.md

sed -i.bak 's|\[user-training/README\.md\](#)|[README.md](#)|g' SHELL-SETUP-GUIDE.md

sed -i.bak 's|\[user-training/1-2-3-ONBOARDING-HOWTO-QUICK-GUIDE\.md\](#)|[1-2-3-ONBOARDING-HOWTO-QUICK-GUIDE.md](#)|g' SHELL-SETUP-GUIDE.md

sed -i.bak 's|\[user-training/CODITECT-TROUBLESHOOTING-GUIDE\.md\](#)|[CODITECT-TROUBLESHOOTING-GUIDE.md](#)|g' SHELL-SETUP-GUIDE.md

cd ../../..

echo "✅ SHELL-SETUP-GUIDE.md updated"

# ===== project-plan.md updates (now in docs/) =====
echo "  → project-plan.md (now in docs/03-project-planning/)..."

cd docs/03-project-planning/

# Update references to TASKLIST if they exist
sed -i.bak 's|\[TASKLIST-WITH-CHECKBOXES\.md\](#)|[tasklist-with-checkboxes.md](#)|g' project-plan.md

# Update references to root README if they exist
sed -i.bak 's|\[README\.md\](#)|[README.md](#)|g' project-plan.md
sed -i.bak 's|\[README\.md\](#)|[README.md](#)|g' project-plan.md

cd ../..

echo "✅ project-plan.md updated"

# ===== TASKLIST updates (now in docs/) =====
echo "  → tasklist-with-checkboxes.md (now in docs/03-project-planning/)..."

cd docs/03-project-planning/

# Update references to PROJECT-PLAN if they exist
sed -i.bak 's|\[PROJECT-PLAN\.md\](#)|[project-plan.md](#)|g' tasklist-with-checkboxes.md

cd ../..

echo "✅ tasklist-with-checkboxes.md updated"

# Remove backup files
find . -name "*.md.bak" -delete

echo ""
echo "✅ All cross-references updated!"
echo ""
echo "🔍 Run validation script to check for broken links..."

📊 Final State Comparison

Before (Current State)

coditect-core/
├── README.md ✅
├── CLAUDE.md ✅
├── AGENT-INDEX.md ❌ (moving to docs/)
├── project-plan.md ❌ (moving to docs/)
├── tasklist-with-checkboxes.md ❌ (moving to docs/)
├── [16 other .md files] ❌ (all moving to docs/)
└── docs/ (33 files, flat structure)

After (Target State)

coditect-core/
├── README.md ✅ ONLY
├── CLAUDE.md ✅ NAVIGATION FILES
└── docs/
    ├── 01-getting-started/
    │   ├── installation/
    │   ├── quick-starts/
    │   └── configuration/
    ├── 02-architecture/
    │   ├── system-design/
    │   └── distributed-intelligence/
    ├── 03-project-planning/
    │   ├── project-plan.md ← MOVED
    │   ├── tasklist-with-checkboxes.md ← MOVED
    │   └── checkpoints/
    ├── 04-implementation-guides/
    │   └── standards/
    ├── multi-agent-reference/
    │   └── AGENT-INDEX.md ← MOVED
    ├── 06-research-analysis/
    │   ├── code-reviews/
    │   ├── completion-reports/
    │   └── gap-analysis/
    └── 09-special-topics/
        ├── memory-context/
        └── legacy/

Production-Ready: ✅ Root has exactly 2 files

✅ Validation

Success Criteria

Migration plan covers all 19 non-essential files
Only README.md and Claude.md remain at root
All files categorized using framework
Git mv preserves history
Cross-references updated (all scripts)
Validation script ready

Execution Checklist

Run directory creation
Execute git mv commands (19 files)
Run link update script
Run validation (0 broken links)
Verify root has exactly 2 .md files
Test README.md navigation
Test Claude.md agent references
Commit with message: "Clean root directory - move all docs to docs/ subdirectories"

🚀 Ready to Execute

Status: ✅ All scripts ready Target: Root with ONLY 2 files (README.md, Claude.md) Files Moving: 19 files Risk: LOW (automated + validated) Time: ~30 minutes

Command to execute

# 1. Run migration
bash ROOT-CLEANUP-MIGRATION-PLAN.md  # (extract script from above)

# 2. Run link updates
bash LINK-UPDATE-SCRIPT.md  # (extract script from above)

# 3. Validate
bash LINK-VALIDATION-SCRIPT.md  # (from orchestrator output)

# 4. Verify root
ls -la *.md  # Should show ONLY README.md and CLAUDE.md

Proceed?

📊 Current State​

📂 Migration Plan by Category​

01-getting-started/ (0 files)​

02-architecture/ (8 files)​

03-project-planning/ (14 files)​

04-implementation-guides/ (8 files)​

multi-agent-reference/ (1 file)​

06-research-analysis/ (7 files)​

07-automation-integration/ (0 files)​

08-training-certification/ (0 files)​

09-special-topics/ (0 files moved - already in subdirectories)​

🔍 Duplicate Files to Remove​

📋 New Subdirectories to Create​

✅ Execution Steps​

📊 Summary​

ROLLOUT-MASTER DOCS MIGRATION ANALYSIS​

📊 Analysis Summary​

Migration Decision​

✅ MOVE to CODITECT-core/docs/ (75 files)​

Category 01: Getting Started (1 file)​

Category 02: Architecture (35 files)​

Vision & Strategy (3 files)​

Architecture Documents (10 files)​

ADRs - Architecture Decision Records (10 files)​

TOON Architecture (12 files)​

Category 03: Project Planning (6 files)​

Core Project Plans (moved from rollout to framework)​

Category 04: Implementation Guides (11 files)​

Category 05: Agent Reference (1 file)​

Category 06: Research & Analysis (6 files)​

Category 09: Special Topics (15 files)​

Memory Context & Deduplication (11 files)​

Submodule Management Framework (4 files)​

⏸️ KEEP in rollout-master/docs/ (18 files)​

Rollout Project Plans (6 files)​

Rollout Timelines (2 files)​

Rollout Task Lists (4 files)​

Rollout Status & Audits (4 files)​

Rollout Submodule Migration (2 files)​

Rollout README​

📋 Migration Execution Plan​

Phase 1: Create Target Directories in CODITECT-core/docs/​

Phase 2: Move Files (75 git mv commands)​

Due to length, migration script will be in separate file​

Phase 3: Update Cross-References​

Phase 4: Create Navigation Files​

📊 Impact Summary​

Before​

After​

Benefits​

Rollout-master becomes​

✅ Validation Checklist​

ROOT DIRECTORY CLEANUP - FINAL MIGRATION PLAN​

🎯 Executive Summary​

Impact​

📋 Complete Migration Plan (19 Files)​

Category 01: Getting Started (4 files)​

Category 02: Architecture (2 files)​

Category 03: Project Planning (3 files) ⭐ UPDATED​

Category 04: Implementation Guides (2 files)​

Category 05: Agent Reference (2 files) ⭐ UPDATED​

Category 06: Research & Analysis (4 files)​

Category 09: Special Topics (2 files)​

🚀 Migration Script (Updated)​

🔗 Updated Cross-Reference Script​

📊 Final State Comparison​

Before (Current State)​

After (Target State)​

✅ Validation​

Success Criteria​

Execution Checklist​

🚀 Ready to Execute​

Command to execute​