version: 3.2.0
python_min_version: '3.10'
dependencies: []
compatibility:
  tested_python:
  - '3.10'
  - '3.11'
  - '3.12'
  - '3.13'
  os:
  - Windows
  - Linux
  - macOS

When to Use

Reorganizing a flat repository structure to module-based layout
Consolidating scattered modules into a unified hierarchy
Standardizing project structure across multiple layers (src, tests, specs, docs, examples)
Migrating import paths while preserving git history
Creating a scalable architecture for growing codebases
Cleaning up root-level artifacts (log files, temp files, build artifacts)
Consolidating duplicate directories (agents/, coordination/, memory/)
Reviewing and removing obsolete hidden folders
Relocating test outputs and prototype code

Pre-flight Checks

CRITICAL: Run these checks before starting any reorganization.

1. Git Tracking Status

# Check what is tracked vs untracked
git ls-files | head -50
git ls-files --others --exclude-standard | head -50

# List all untracked files at root level
git ls-files --others --exclude-standard | grep -v "/"

# Check for ignored files that might need cleanup
git status --ignored

2. Duplicate Directory Detection

# Find duplicate agent directories
ls -la agents/ .claude/agents/ .claude/agent-library/ 2>/dev/null

# Find duplicate coordination/memory directories

# Find duplicate skill locations
find . -type d -name "skills" 2>/dev/null

3. Identify Runtime vs Config Files

# Runtime data (should NOT be in git)
find . -name "*.log" -o -name "*.tmp" -o -name "__pycache__" 2>/dev/null

# Config files (SHOULD be in git)
find . -name "*.json" -o -name "*.yaml" -o -name "*.toml" 2>/dev/null | head -30

# Large files that might be test data
find . -size +1M -type f 2>/dev/null

4. Hidden Folder Inventory

# List all hidden folders at root
ls -la .* 2>/dev/null | grep "^d"

# Common hidden folders to review:
# .agent-os/     - May contain duplicate agent configs
# .ai/           - Legacy AI coordination
# .drcode/       - DR Code artifacts
# .claude/       - Claude configuration (KEEP)
# .git/          - Git data (KEEP)
# .venv/         - Virtual environment (should be ignored)

5. Identify Stale Artifacts

# Find log files in root
ls *.log 2>/dev/null

# Find test output files
ls *_output.* test_*.txt *.html 2>/dev/null

# Find build artifacts
ls *.egg-info dist/ build/ 2>/dev/null

Pre-consolidation Analysis

Before merging hidden folders, perform a thorough analysis to understand scope and identify conflicts.

1. Count Tracked Files per Hidden Folder

# Count tracked files in each hidden folder
git ls-files .claude/ | wc -l
git ls-files .agent-os/ | wc -l
git ls-files .ai/ | wc -l

# Example output:
# .claude/: 519 files
# .agent-os/: 129 files
# .ai/: 52 files
# Total after merge: 519 + 129 + 52 = 700 files (minus overlaps)

2. Identify Overlapping Content

# Compare directory structures
ls -la .claude/ .agent-os/ .ai/ 2>/dev/null

# Find common subdirectory names
comm -12 <(ls .claude/ | sort) <(ls .agent-os/ | sort)
comm -12 <(ls .claude/ | sort) <(ls .ai/ | sort)

# Common overlap patterns:
# - commands/ in both .claude/ and .agent-os/
# - hooks/ in both .claude/ and .agent-os/
# - docs/ in multiple locations

3. Determine Authoritative Source

# Check which folder has more recent commits
git log --oneline -5 -- .claude/
git log --oneline -5 -- .agent-os/
git log --oneline -5 -- .ai/

# Check file modification dates
find .claude/ -type f -printf '%T+ %p\n' | sort -r | head -10
find .agent-os/ -type f -printf '%T+ %p\n' | sort -r | head -10

# Check for unique content in each folder
diff -rq .claude/docs/ .agent-os/docs/ 2>/dev/null | head -20

4. Create Merge Plan

Based on analysis, plan the merge strategy:

Source Folder	Destination	Strategy	Reason
.agent-os/commands/	.claude/commands/legacy-scripts/	Rename to avoid conflict	.claude/commands/ already exists
.agent-os/hooks/	.claude/hooks/legacy/	Rename to avoid conflict	.claude/hooks/ already exists
.agent-os/docs/	.claude/docs/	Merge	Unique documentation content
.agent-os/standards/	.claude/standards/	Copy (new)	Does not exist in .claude/
.ai/implementation-history/	.claude/implementation-history/	Copy (new)	Unique content
Conflicting README.md	README-legacy.md	Rename	Preserve both versions

Parallel Execution Strategy

Agent Spawn Patterns

Use parallel subagents for faster reorganization. Tasks that don't have dependencies can run simultaneously.

Phase 1: Analysis (PARALLEL)

// All analysis tasks can run in parallel
Task("Analyze source structure", "List all directories in src/ and identify modules vs infrastructure", "explorer")
Task("Analyze test structure", "List all directories in tests/ and identify test modules", "explorer")
Task("Analyze specs/docs", "List all directories in specs/ and docs/", "explorer")
Task("Inventory root artifacts", "List all files at root level, identify logs/temp/build artifacts", "explorer")
Task("Hidden folder audit", "List all hidden folders, check git tracking status", "explorer")

Phase 2: Directory Creation (SEQUENTIAL)

# Must be sequential - directories must exist before moves
mkdir -p src/<package>/modules
mkdir -p tests/modules
mkdir -p specs/modules
mkdir -p docs/modules
mkdir -p examples/modules

Phase 3: Module Moves (PARALLEL by module)

// Each module can be moved in parallel (no cross-dependencies)
Task("Move aqwa module", "git mv all aqwa files across 5 layers", "coder")
Task("Move catenary module", "git mv all catenary files across 5 layers", "coder")
Task("Move orcaflex module", "git mv all orcaflex files across 5 layers", "coder")
Task("Move mooring module", "git mv all mooring files across 5 layers", "coder")

Phase 3.5: Hidden Folder Consolidation (PARALLEL by folder)

// Each hidden folder can be consolidated in parallel (no cross-dependencies)
Task("Consolidate .agent-os", "Merge .agent-os/ into .claude/ with conflict resolution", "Bash")
Task("Consolidate .ai", "Merge .ai/ into .claude/ preserving unique content", "Bash")
Task("Consolidate .drcode", "Review and merge .drcode/ artifacts if valuable", "Bash")

Consolidation Commands Pattern:

# Phase 3.5a: Consolidate .agent-os/ (129 files)
# Move conflicting directories with rename
git mv .agent-os/commands .claude/commands/legacy-scripts
git mv .agent-os/hooks .claude/hooks/legacy

# Move non-conflicting directories directly
git mv .agent-os/standards .claude/standards
git mv .agent-os/docs/* .claude/docs/

# Handle conflicting README
git mv .agent-os/README.md .claude/README-agent-os-legacy.md

# Phase 3.5b: Consolidate .ai/ (52 files)
# Move unique content
git mv .ai/implementation-history .claude/implementation-history
git mv .ai/docs/* .claude/docs/

# Handle conflicting README
git mv .ai/README.md .claude/README-ai-legacy.md

# Phase 3.5c: Remove empty source folders
rm -rf .agent-os/ .ai/

Phase 4: Import Updates (PARALLEL by file type)

// Import updates can be parallelized by file type
Task("Update source imports", "Update imports in src/**/*.py", "coder")
Task("Update test imports", "Update imports in tests/**/*.py", "coder")
Task("Update example imports", "Update imports in examples/**/*.py", "coder")

Phase 5: Cleanup (PARALLEL)

// Cleanup tasks are independent
Task("Remove root artifacts", "Delete log files, temp files from root", "coder")
Task("Consolidate agent dirs", "Move agents/ content to .claude/agent-library/", "coder")
Task("Clean hidden folders", "Remove obsolete .agent-os/, .ai/, .drcode/", "coder")
Task("Update .gitignore", "Add runtime data patterns to .gitignore", "coder")

Phase 6: Verification (PARALLEL then SEQUENTIAL)

// Parallel verification
Task("Verify imports", "Test all import statements work", "tester")
Task("Verify git status", "Check git status is clean, no broken files", "tester")
Task("Run test suite", "Run pytest to verify nothing broken", "tester")

// Sequential final review
Task("Final structure review", "Compare actual structure to target structure", "reviewer")

Parallel vs Sequential Decision Matrix

Task Type	Parallel?	Reason
Analysis/Inventory	YES	Read-only, no conflicts
Directory creation	NO	Order matters for parent dirs
Module moves (same module)	NO	Files may reference each other
Module moves (different modules)	YES	Independent file sets
Hidden folder consolidation	YES	Each folder merged independently
Import updates (same file)	NO	Would cause conflicts
Import updates (different files)	YES	No file conflicts
Cleanup tasks	YES	Independent operations
Test execution	NO	May have shared fixtures
Verification	MIXED	Some parallel, final review sequential

Target Structure

The 5-layer module architecture:

src/<package>/modules/<module_name>/
tests/modules/<module_name>/
specs/modules/<module_name>/
docs/modules/<module_name>/
examples/modules/<module_name>/

Example: digitalmodel Package

src/digitalmodel/modules/
├── __init__.py
├── aqwa/
│   ├── __init__.py
│   ├── aqwa_reader.py
│   └── aqwa_utilities.py
├── catenary/
│   ├── __init__.py
│   ├── catenary.py
│   └── catenary_riser.py
├── fea_model/
│   ├── __init__.py
│   └── line_components.py
├── mooring/
│   ├── __init__.py
│   └── mooring.py
├── orcaflex/
│   ├── __init__.py
│   └── OrcaFlexAnalysis.py
└── pipe_capacity/
    ├── __init__.py
    └── custom/

tests/modules/
├── conftest.py
├── aqwa/
│   └── test_aqwa_reader.py
├── catenary/
│   └── test_catenary.py
└── orcaflex/
    └── test_orcaflex_analysis.py

specs/modules/
├── .gitkeep
├── aqwa/
│   └── spec.md
└── orcaflex/
    └── spec.md

docs/modules/
├── aqwa/
│   └── README.md
└── orcaflex/
    └── README.md

examples/modules/
├── aqwa/
│   └── basic_analysis.py
└── orcaflex/
    └── batch_processing.py

Process

Phase 1: Analysis

List all top-level directories

ls -la src/<package>/
ls -la tests/
ls -la specs/

Identify modules vs infrastructure
- Modules: Domain-specific code directories (e.g., aqwa/, catenary/, orcaflex/)
- Infrastructure: Support directories that should stay at root level

Document current state

# List all Python files to understand module scope
find src/<package> -name "*.py" -type f | head -50

# Check for existing module imports
grep -r "from <package>" --include="*.py" . | head -20

Phase 2: Planning

Create migration plan
- List all modules to be moved
- Identify dependencies between modules
- Plan import path changes

Identify infrastructure folders (keep at root)

# Tests infrastructure
tests/test_data/
tests/test_configs/
tests/fixtures/
tests/conftest.py (root level)

# Specs infrastructure
specs/templates/
specs/features/

# Project infrastructure
config/
scripts/
.claude/

Phase 3: Create Target Directories

# Create module directories with git-tracked placeholders
mkdir -p src/<package>/modules
mkdir -p tests/modules
mkdir -p specs/modules
mkdir -p docs/modules
mkdir -p examples/modules

# Add .gitkeep for empty directories
touch specs/modules/.gitkeep
touch docs/modules/.gitkeep
touch examples/modules/.gitkeep

Phase 4: Move with Git History Preservation

CRITICAL: Always use git mv to preserve history.

# Move source modules
git mv src/<package>/<module> src/<package>/modules/<module>

# Move test modules
git mv tests/<module> tests/modules/<module>

# Move spec modules
git mv specs/<module> specs/modules/<module>

# Move doc modules
git mv docs/<module> docs/modules/<module>

# Move example modules
git mv examples/<module> examples/modules/<module>

Example: Moving aqwa module

# Source
git mv src/digitalmodel/aqwa src/digitalmodel/modules/aqwa

# Tests
git mv tests/aqwa tests/modules/aqwa

# Specs (if exists)
git mv specs/aqwa specs/modules/aqwa

# Docs (if exists)
git mv docs/aqwa docs/modules/aqwa

Phase 5: Update Imports

Search for old import patterns

# Find all files with old import paths
grep -r "from <package>.<module>" --include="*.py" .
grep -r "import <package>.<module>" --include="*.py" .

Update import statements

# Update imports (example using sed)
find . -name "*.py" -exec sed -i 's/from digitalmodel.aqwa/from digitalmodel.modules.aqwa/g' {} \;
find . -name "*.py" -exec sed -i 's/import digitalmodel.aqwa/import digitalmodel.modules.aqwa/g' {} \;

Common import transformations

# Before
from digitalmodel.aqwa import aqwa_reader
from digitalmodel.catenary.catenary import Catenary

# After
from digitalmodel.modules.aqwa import aqwa_reader
from digitalmodel.modules.catenary.catenary import Catenary

Phase 6: Create init.py Files

Module root init.py

# src/<package>/modules/__init__.py
"""
Module-based architecture for <package>.

Available modules:
- aqwa: AQWA hydrodynamic analysis
- catenary: Catenary riser analysis
- fea_model: FEA model components
- mooring: Mooring system analysis
- orcaflex: OrcaFlex simulation
- pipe_capacity: Pipe capacity calculations
"""

from digitalmodel.modules import aqwa
from digitalmodel.modules import catenary
from digitalmodel.modules import fea_model
from digitalmodel.modules import mooring
from digitalmodel.modules import orcaflex
from digitalmodel.modules import pipe_capacity

__all__ = [
    "aqwa",
    "catenary",
    "fea_model",
    "mooring",
    "orcaflex",
    "pipe_capacity",
]

Individual module init.py

# src/<package>/modules/<module>/__init__.py
"""
<Module Name> - Brief description.

Key classes and functions exported from this module.
"""

from digitalmodel.modules.<module>.<main_file> import MainClass
from digitalmodel.modules.<module>.<utils_file> import utility_function

__all__ = ["MainClass", "utility_function"]

Phase 7: Verification

Test imports work

# test_imports.py
import sys
sys.path.insert(0, 'src')

# Test new import paths
from digitalmodel.modules.aqwa import aqwa_reader
from digitalmodel.modules.catenary.catenary import Catenary
from digitalmodel.modules.orcaflex import OrcaFlexAnalysis

print("All imports successful!")

Run test suite
```
uv run pytest tests/ -v
```

Check for broken imports

# Find any remaining old import patterns
grep -r "from digitalmodel\." --include="*.py" . | grep -v "modules"

Checklist

Pre-Refactor

Git working directory is clean
All tests pass before refactor
Created backup branch
Documented current structure
Pre-flight checks completed (see Pre-flight Checks section)
Duplicate directories identified
Runtime vs config files categorized
Hidden folders inventoried

During Refactor

Module Structure

All modules moved to modules/ subdirectory using git mv
tests/modules/ created and populated
specs/modules/ created (with .gitkeep if empty)
docs/modules/ created (with .gitkeep if empty)
examples/modules/ created (with .gitkeep if empty)

Root-Level Artifact Cleanup

Log files removed (*.log)
Temp files removed (*.tmp, *.temp)
Build artifacts removed (dist/, build/, *.egg-info/)
Cache files removed (pycache/, .pytest_cache/)
Test output files relocated or removed
Prototype/experimental code relocated to examples/ or removed

Directory Consolidation

agents/ content moved to .claude/agent-library/
Duplicate skill directories merged
Empty directories removed

Hidden Folder Review

.agent-os/ - reviewed and cleaned (usually remove)
.ai/ - reviewed and cleaned (usually remove)
.drcode/ - reviewed and cleaned (usually remove)
.claude/ - kept and organized
.venv/ - confirmed in .gitignore

Test Output Relocation

HTML reports moved to tests/reports/ or removed
Coverage reports moved to tests/coverage/ or removed
Screenshot outputs moved to tests/snapshots/ or removed
Benchmark results moved to tests/benchmarks/ or removed

Plan File Archival

Completed plan files archived to specs/archive/
Plan files checked for status: completed in YAML frontmatter

Benchmark Reorganization

Benchmark test fixtures moved to tests/fixtures/<tool_name>/
Benchmark generated outputs (reports/, results/) added to .gitignore
Empty benchmark structure maintained with .gitkeep

Post-Refactor

__init__.py files created with proper exports
All import references updated
pyproject.toml updated if needed
Tests pass after refactor
No broken imports found
Git history preserved (verify with git log --follow)
Post-cleanup verification completed (see Post-cleanup Verification section)
.gitignore updated with new patterns
No untracked files at root level (except intended ones)

Common Patterns Found During Reorganization

Based on real-world reorganization experience, these patterns frequently appear:

1. Duplicate Agent Directories

# Pattern: Multiple locations for agent definitions
agents/                          # Root-level (often untracked)
.claude/agents/                  # Claude-specific
.claude/agent-library/           # Preferred location
.agent-os/agents/                # Legacy AI OS structure

# Resolution: Consolidate to .claude/agent-library/
git mv agents/* .claude/agent-library/
rm -rf agents/

2. Scattered Runtime Data

# Pattern: Runtime data mixed with config
coordination/                    # Untracked runtime state
memory/                          # Untracked memory store

# Resolution:
# - Delete untracked coordination/ and memory/

3. Untracked Artifacts in Root

# Pattern: Various artifacts accumulate in root
*.log                            # Log files from various tools
*.html                           # Test reports, visualizations
*_output.*                       # Output files from scripts
*.sim                            # Simulation files
*.dat                            # Data files

# Resolution:
# - Delete if not needed
# - Move to inputs/ or outputs/ if needed
# - Add patterns to .gitignore

4. Multiple Skill/Command Locations

# Pattern: Skills defined in multiple places
.claude/skills/                  # Claude skills
skills/                          # Root-level skills
.agent-os/skills/                # Legacy location
commands/                        # Alternative naming

# Resolution: Consolidate to .claude/skills/

5. Legacy Hidden Folders

# Pattern: Accumulation of AI tool folders
.agent-os/                       # Custom agent OS (usually obsolete)
.ai/                             # Generic AI folder
.drcode/                         # DR Code specific
.cursor/                         # Cursor editor
.vscode/                         # VS Code settings

# Resolution:
# - .vscode/, .cursor/ - keep if used, add to .gitignore
# - .agent-os/, .ai/, .drcode/ - usually safe to remove
# - Check for any unique configs before deleting

6. Test Data in Wrong Locations

# Pattern: Test data scattered
tests/test_data/                 # Correct location
test_data/                       # Root level (wrong)
data/                            # Ambiguous location
fixtures/                        # Sometimes at root

# Resolution: Move all to tests/test_data/ or tests/fixtures/

7. Prototype Code Mixed with Production

# Pattern: Experimental code in src/
src/package/experimental/        # Should be separate
src/package/prototype_*.py       # Should be in examples/
scripts/scratch_*.py             # Should be in examples/experiments/

# Resolution: Move to examples/experiments/ or examples/prototypes/

Hidden Folder Consolidation Patterns

When consolidating multiple hidden folders into a single authoritative location (.claude/), follow these patterns based on real-world experience.

Real-World Example: digitalmodel Repository

Before consolidation:

.claude/      519 tracked files (authoritative)
.agent-os/    129 tracked files (legacy)
.ai/           52 tracked files (legacy)

After consolidation:

.claude/      670 tracked files (519 + 129 + 52, minus duplicates)

Merge Patterns by Content Type

1. Conflicting Directories (Rename to Preserve Both)

# When both source and destination have the same directory name
# Pattern: Move to a subdirectory with 'legacy-' prefix

# commands/ exists in both .agent-os/ and .claude/
git mv .agent-os/commands .claude/commands/legacy-scripts

# hooks/ exists in both .agent-os/ and .claude/
git mv .agent-os/hooks .claude/hooks/legacy

# Result: Original .claude/commands/ preserved, .agent-os/commands/ accessible at legacy-scripts/

2. Non-Conflicting Directories (Direct Move)

# When destination doesn't have the directory
# Pattern: Direct git mv

# standards/ only exists in .agent-os/
git mv .agent-os/standards .claude/standards

# implementation-history/ only exists in .ai/
git mv .ai/implementation-history .claude/implementation-history

# Result: Clean move preserving git history

3. Mergeable Directories (Combine Content)

# When both have the same directory with different files
# Pattern: Move individual files or use merge strategy

# docs/ has different files in each location
git mv .agent-os/docs/unique-file.md .claude/docs/
git mv .ai/docs/another-file.md .claude/docs/

# Or merge entire directories (may require manual review)
cp -r .agent-os/docs/* .claude/docs/
git add .claude/docs/
git rm -r .agent-os/docs/

4. Conflicting Files (Rename with Suffix)

# When same filename exists in multiple locations
# Pattern: Rename with source identifier

# README.md exists in .claude/, .agent-os/, and .ai/
git mv .agent-os/README.md .claude/README-agent-os-legacy.md
git mv .ai/README.md .claude/README-ai-legacy.md

# Or use descriptive names
git mv .agent-os/README.md .claude/docs/agent-os-overview.md
git mv .ai/README.md .claude/docs/ai-folder-overview.md

Consolidation Checklist

Count files in each source folder: git ls-files <dir> | wc -l
Identify overlapping directory names
Identify overlapping file names
Create merge plan with conflict resolution strategy
Execute moves in parallel per source folder
Verify no files were lost: compare totals
Remove empty source folders
Update any references to old paths
Commit with descriptive message noting file counts

Common Consolidation Scenarios

Scenario	Source	Destination	Strategy
Duplicate commands	.agent-os/commands/	.claude/commands/legacy-scripts/	Rename
Duplicate hooks	.agent-os/hooks/	.claude/hooks/legacy/	Rename
Unique standards	.agent-os/standards/	.claude/standards/	Direct move
Unique history	.ai/implementation-history/	.claude/implementation-history/	Direct move
Overlapping docs	.agent-os/docs/	.claude/docs/	Merge content
Conflicting README	.agent-os/README.md	.claude/README-legacy.md	Rename

Metrics Tracking

Track quantitative metrics throughout the consolidation process to verify completeness and document changes.

Pre-consolidation Metrics

# Capture baseline metrics before any changes
echo "=== Pre-consolidation File Counts ==="
echo ".claude/: $(git ls-files .claude/ | wc -l) files"
echo ".agent-os/: $(git ls-files .agent-os/ | wc -l) files"
echo ".ai/: $(git ls-files .ai/ | wc -l) files"
echo "Total: $(git ls-files .claude/ .agent-os/ .ai/ | wc -l) files"

# Save to file for comparison
git ls-files .claude/ .agent-os/ .ai/ | wc -l > /tmp/pre_consolidation_count.txt

Post-consolidation Verification

# Verify file counts after consolidation
echo "=== Post-consolidation File Counts ==="
echo ".claude/: $(git ls-files .claude/ | wc -l) files"

# Compare to expected total
expected=$(cat /tmp/pre_consolidation_count.txt)
actual=$(git ls-files .claude/ | wc -l)
echo "Expected: $expected files"
echo "Actual: $actual files"

if [ "$actual" -ge "$expected" ]; then
    echo "SUCCESS: All files accounted for"
else
    echo "WARNING: $(($expected - $actual)) files may be missing"
fi

Git Commit Metrics

# Check what the commit will include
git diff --stat --staged

# Example output:
# 181 files changed, 2847 insertions(+), 1523 deletions(-)

# The numbers indicate:
# - files changed: Total files moved/renamed
# - insertions: Lines added (includes moved content)
# - deletions: Lines removed (includes content moved from old location)

Metrics Documentation Template

Document consolidation metrics in commit message or notes:

## Consolidation Metrics

**Operation**: Hidden folder consolidation to .claude/

**File Counts**:
- Before: .claude/ (519) + .agent-os/ (129) + .ai/ (52) = 700 total
- After: .claude/ (670 files)
- Difference: 30 files were duplicates/merged

**Git Stats**: 181 files changed, +2847/-1523 lines

**Decisions Made**:
- Moved: 151 files (no conflicts)
- Renamed: 25 files (conflict resolution)
- Merged: 5 files (content combined)
- Deleted: 0 files (none removed)

**Source Folders Removed**:
- .agent-os/ (fully merged)
- .ai/ (fully merged)

Tracking Delete vs Move Decisions

# Create a decision log during consolidation
cat > consolidation_log.md << 'EOF'
# Consolidation Decision Log

| File/Directory | Action | Reason |
|----------------|--------|--------|
| .agent-os/commands/ | MOVED to .claude/commands/legacy-scripts/ | Conflict with existing |
| .agent-os/standards/ | MOVED to .claude/standards/ | No conflict |
| .agent-os/temp/ | DELETED | Runtime data, not needed |
| .ai/implementation-history/ | MOVED to .claude/implementation-history/ | Unique valuable content |
| .ai/.cache/ | DELETED | Cache data, regenerated |
EOF

# Track in git for documentation
git add consolidation_log.md

Post-cleanup Verification

1. Import Verification for Python Modules

# Create a verification script
cat > verify_imports.py << 'EOF'
#!/usr/bin/env python
"""Verify all imports work after reorganization."""
import sys
from pathlib import Path

# Add src to path
sys.path.insert(0, str(Path(__file__).parent / "src"))

# Test all module imports
modules_to_test = [
    "digitalmodel",
    "digitalmodel.modules",
    "digitalmodel.modules.aqwa",
    "digitalmodel.modules.catenary",
    "digitalmodel.modules.orcaflex",
    "digitalmodel.modules.mooring",
    "digitalmodel.modules.fea_model",
    "digitalmodel.modules.pipe_capacity",
]

failed = []
for module in modules_to_test:
    try:
        __import__(module)
        print(f"✓ {module}")
    except ImportError as e:
        print(f"✗ {module}: {e}")
        failed.append(module)

if failed:
    print(f"\n{len(failed)} imports failed!")
    sys.exit(1)
else:
    print(f"\nAll {len(modules_to_test)} imports successful!")
EOF

# Run verification
uv run python verify_imports.py

2. Git Status Review

# Check for any unintended changes
git status

# Verify no broken file references
git diff --name-status

# Check for files that should be tracked but aren't
git ls-files --others --exclude-standard

# Verify history preservation for moved files
git log --follow --oneline -- src/digitalmodel/modules/aqwa/aqwa_reader.py

3. Directory Structure Validation

# Verify target structure exists
echo "=== Source Modules ==="
ls -la src/digitalmodel/modules/

echo "=== Test Modules ==="
ls -la tests/modules/

echo "=== Spec Modules ==="
ls -la specs/modules/

echo "=== Doc Modules ==="
ls -la docs/modules/

echo "=== Example Modules ==="
ls -la examples/modules/

# Verify no modules remain at old locations
echo "=== Check for stragglers ==="
ls src/digitalmodel/ | grep -v "modules\|__\|\.py"

4. Test Suite Execution

# Run full test suite
uv run pytest tests/ -v

# Run with coverage to verify all code is reachable
uv run pytest tests/ --cov=src/digitalmodel --cov-report=term-missing

# Run specific module tests
uv run pytest tests/modules/aqwa/ -v

5. Clean Root Verification

# List root directory contents - should be minimal
ls -la | grep -v "^d" | grep -v "^\."

# Expected root files:
# - pyproject.toml
# - README.md
# - LICENSE
# - .gitignore
# - CLAUDE.md (optional)

# Anything else should be questioned

6. Gitignore Verification

# Check .gitignore has all necessary patterns

# Recommended patterns to add:
# *.log
# *.tmp
# __pycache__/
# .pytest_cache/
# dist/
# build/
# *.egg-info/
# .coverage
# htmlcov/

Common Issues and Solutions

Issue: Circular imports after refactor

Solution: Use lazy imports or restructure dependencies

# Use TYPE_CHECKING for type hints only
from typing import TYPE_CHECKING
if TYPE_CHECKING:
    from digitalmodel.modules.other import OtherClass

Issue: Relative imports broken

Solution: Convert to absolute imports

# Before (relative)
from .utils import helper

# After (absolute)
from digitalmodel.modules.mymodule.utils import helper

Issue: Test discovery fails

Solution: Ensure conftest.py at tests/modules/ level

# tests/modules/conftest.py
import sys
from pathlib import Path

# Add src to path for imports
src_path = Path(__file__).parent.parent.parent / "src"
sys.path.insert(0, str(src_path))

Issue: Package not found after move

Solution: Update pyproject.toml package discovery

[tool.setuptools.packages.find]
where = ["src"]
include = ["digitalmodel*"]

Best Practices

Commit frequently - Make small, focused commits for each module moved
Use feature branch - Create refactor/module-structure branch
Update documentation - Update README.md and any architecture docs
Communicate changes - If team project, document breaking changes
Run full test suite - Verify all tests pass before merging

Related Skills

context-management - Managing context during large refactors
session-start-routine - Session initialization

References

Python Packaging Guide: https://packaging.python.org/
Git mv documentation: https://git-scm.com/docs/git-mv
PEP 420 - Implicit Namespace Packages

Cleanup Categories Quick Reference

Category	Examples	Action
Root-level artifacts	.log, .tmp, *.html	Delete or move to outputs/
Build artifacts	dist/, build/, *.egg-info	Delete (regenerated on build)
Cache files	pycache/, .pytest_cache/	Delete and .gitignore
Duplicate dirs	agents/, .claude/agents/	Consolidate to .claude/agent-library/
Legacy hidden	.agent-os/, .ai/, .drcode/	Review and usually delete
Test outputs	reports/, coverage/, snapshots/	Move under tests/
Prototype code	scratch_*.py, experimental/	Move to examples/
Test data	.csv, .json at root	Move to tests/test_data/
Config files	.yaml, .toml, *.json	Keep at root or move to config/
Benchmark fixtures	legacy test data files	Move to tests/fixtures/<tool_name>/
Benchmark outputs	timestamped reports/results	Add to .gitignore
Completed plans	status: completed in frontmatter	Archive to specs/archive/

Benchmark Directory Reorganization

Benchmark directories often contain mixed content: test fixtures that should be tracked vs generated outputs that should be ignored.

Pattern: Separate Tracked Fixtures from Gitignored Outputs

# 1. Identify benchmark content types
ls -la benchmarks/

# Common benchmark content:
# - legacy_projects/     -> Test fixtures (track in git)
# - reports/             -> Generated HTML reports (gitignore)
# - results/             -> Generated CSV/JSON results (gitignore)

# 2. Move test fixtures to tests/fixtures/
git mv benchmarks/legacy_projects/ tests/fixtures/orcaflex/

# 3. Add generated output directories to .gitignore
cat >> .gitignore << 'EOF'

# Benchmark generated outputs
benchmarks/reports/
benchmarks/results/
EOF

# 4. Create .gitkeep for empty benchmark structure
mkdir -p benchmarks/reports benchmarks/results
touch benchmarks/.gitkeep

Benchmark Content Classification

Content Type	Examples	Action
Test fixtures	legacy_projects/.dat, reference_data/.csv	`git mv` to tests/fixtures/<tool_name>/
Generated reports	report_YYYYMMDD.html, benchmark.html	Add to .gitignore
Generated results	results_YYYYMMDD.csv, output_*.json	Add to .gitignore
Benchmark scripts	run_benchmarks.py, compare_results.py	Keep in benchmarks/ or scripts/benchmarks/

Example: OrcaFlex Benchmark Reorganization

# Before:
benchmarks/
├── legacy_projects/          # Test fixture OrcaFlex files (tracked)
│   ├── model1.dat
│   └── model2.dat
├── reports/                  # Generated HTML reports (untracked)
│   └── benchmark_20260120.html
└── results/                  # Generated CSV results (untracked)
    └── results_20260120.csv

# After:
tests/fixtures/orcaflex/      # Moved from benchmarks/legacy_projects/
├── model1.dat
└── model2.dat

benchmarks/                   # Clean benchmark directory
├── .gitkeep
├── reports/                  # .gitignore'd
└── results/                  # .gitignore'd

Complete Refactor Session Workflow

A full repository refactor typically follows this 4-phase workflow. Each phase should be committed separately for clean git history and easy rollback.

Phase 1: Module Reorganization

Move code to the 5-layer module-based architecture.

# 1a. Move source modules
git mv src/<pkg>/<module> src/<pkg>/modules/<module>

# 1b. Move tests
git mv tests/<module> tests/modules/<module>

# 1c. Move specs
git mv specs/<module> specs/modules/<module>

# 1d. Update imports across codebase
find . -name "*.py" -exec sed -i 's/from <pkg>.<module>/from <pkg>.modules.<module>/g' {} \;

# 1e. Commit Phase 1
git commit -m "refactor: Reorganize repository to module-based 5-layer architecture"

Phase 2: Hidden Folder Consolidation

Merge legacy AI/agent folders into .claude/.

# 2a. Consolidate .agent-os/ + .ai/ into .claude/
# Example: 519 + 129 + 52 = 670 files after merge
git mv .agent-os/commands .claude/commands/legacy-scripts
git mv .agent-os/standards .claude/standards
git mv .ai/implementation-history .claude/implementation-history

# 2b. Delete dead folders
rm -rf .agent-runtime .common .specify

# 2c. Commit Phase 2
git commit -m "refactor: Consolidate .agent-os + .ai into .claude (670 files)"

Phase 3: Final Cleanup

Remove legacy configurations and consolidate scripts.

# 3a. Delete legacy config folders
rm -rf .drcode/        # Legacy AI config (confirmed deletable)
rm -rf .benchmarks/    # Empty benchmark folder

# 3b. Consolidate scripts
git mv .git-commands/* scripts/git/
rm -rf .git-commands/

# 3c. Move registries to docs
git mv .slash-commands/* .claude/docs/commands/
rm -rf .slash-commands/

# 3d. Commit Phase 3
git commit -m "chore: Delete legacy config and consolidate scripts"

Phase 4: Documentation and Archival

Update README and skill documentation with learnings. Archive completed plans.

# 4a. Update README structure section
# - Document new module-based architecture
# - Remove references to deleted folders

# 4b. Update skills with session learnings
# - Add new patterns discovered
# - Update version numbers
# - Add changelog entries

# 4c. Archive completed plan files
# Check plan files in specs/modules/ for status: completed in YAML frontmatter
# Move completed plans to specs/archive/ to keep specs/modules/ clean
git mv specs/modules/<completed-plan>.md specs/archive/

# 4d. Commit Phase 4
git commit -m "docs: Update README structure and skill documentation"

Plan File Archival Pattern

Completed plans in specs/modules/ should be archived to maintain a clean working directory.

# Check plan file YAML frontmatter for completion status
grep -l "status: completed" specs/modules/*.md

# Archive completed plans using git mv to preserve history
git mv specs/modules/<completed-plan>.md specs/archive/

# Example: Archive a completed refactor plan
git mv specs/modules/module-based-refactor-plan.md specs/archive/

# Verify archive directory exists
mkdir -p specs/archive

When to Archive:

Plan file has status: completed in YAML frontmatter
All tasks in the plan have been implemented and verified
The refactor session is complete and committed

Commit Strategy: Atomic Commits Per Phase

Phase	Commit Message Pattern	Scope
1	`refactor: Reorganize repository to module-based 5-layer architecture`	src, tests, specs, imports
2	`refactor: Consolidate <folders> into .claude (N files)`	Hidden folder merges
3	`chore: Delete legacy config and consolidate scripts`	Cleanup operations
4	`docs: Update README structure and skill documentation`	Documentation updates

Benefits of Atomic Commits:

Easy to review changes in each phase
Simple rollback if issues discovered
Clear git history for future reference
Supports incremental verification after each phase

Quick Start Commands

# 1. Pre-flight check (run first)
git status && git ls-files --others --exclude-standard | wc -l

# 2. Find all hidden folders
ls -la .* 2>/dev/null | grep "^d"

# 3. Find duplicates
find . -type d -name "agents" -o -name "skills" -o -name "memory" 2>/dev/null

# 4. Find artifacts at root
ls *.log *.tmp *.html *.sim 2>/dev/null

# 5. Create module structure
mkdir -p src/<pkg>/modules tests/modules specs/modules docs/modules examples/modules

# 6. Archive completed plan files
git mv specs/modules/<completed-plan>.md specs/archive/

# 7. Verify after cleanup
uv run pytest tests/ -v && git status

Version History

3.2.0 (2026-01-20): Added Plan File Archival and Benchmark Reorganization patterns
- Added Plan File Archival pattern to archive completed plans to specs/archive/
- Added Benchmark Directory Reorganization pattern for separating fixtures from outputs
- Added benchmark-related gitignore patterns (reports/, results/)
- Updated checklist with plan archival and benchmark reorganization items
- Updated Quick Start Commands with plan archival command
- Updated Phase 4 to include archival step
3.1.0 (2026-01-20): Added Complete Refactor Session Workflow
- Added 4-phase workflow documentation (Module Reorganization, Hidden Folder Consolidation, Final Cleanup, Documentation)
- Added Commit Strategy section with atomic commits per phase pattern
- Documented real-world session flow with specific examples
- Added benefits of atomic commits for review, rollback, and history
3.0.0 (2026-01-20): Major update with hidden folder consolidation patterns
- Added Pre-consolidation Analysis section for analyzing hidden folder overlaps
- Added Hidden Folder Consolidation Patterns section with real-world examples
- Added Phase 3.5: Hidden Folder Consolidation to Parallel Execution Strategy
- Added Metrics Tracking section for quantitative verification
- Added merge patterns: Conflicting Directories, Non-Conflicting Directories, Mergeable Directories, Conflicting Files
- Added Consolidation Checklist and Common Consolidation Scenarios table
- Added Metrics Documentation Template for commit messages
- Updated Parallel vs Sequential Decision Matrix with hidden folder consolidation
- Real-world example: .agent-os/ (129 files) + .ai/ (52 files) merged into .claude/ (519 -> 670 files)
2.0.0 (2025-01-20): Major update with comprehensive cleanup categories
- Added Pre-flight Checks section
- Added Parallel Execution Strategy with agent spawn patterns
- Added Common Patterns Found During Reorganization
- Added Post-cleanup Verification section
- Expanded Checklist with cleanup categories
- Added Quick Reference tables and Quick Start commands
1.0.0 (2025-01-19): Initial release based on digitalmodel repository refactor experience

module-based-refactor

Module-Based Refactor Skill

Version Metadata

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