version: 2.2.0
python_min_version: '3.10'
dependencies: []
compatibility:
  tested_python:
  - '3.10'
  - '3.11'
  - '3.12'
  - '3.13'
  os:
  - Windows
  - Linux
  - macOS

# Find all build artifacts
find . -type d -name "__pycache__" -o -name "*.egg-info" -o -name ".pytest_cache"

# Remove Python cache (safe - regenerated automatically)
find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null
find . -type d -name "*.egg-info" -exec rm -rf {} + 2>/dev/null
find . -type d -name ".pytest_cache" -exec rm -rf {} + 2>/dev/null

# Find log files
find . -name "*.log" -o -name "*LogFile.txt"

# Remove log files (verify first)
find . -name "*.log" -type f -delete
find . -name "*LogFile.txt" -type f -delete

# Find temp files
find . -name "*.tmp" -o -name "*.bak" -o -name "*.swp" -o -name "*~"

# Remove temp files
find . \( -name "*.tmp" -o -name "*.bak" -o -name "*.swp" -o -name "*~" \) -type f -delete

# Remove coverage artifacts
rm -rf htmlcov/
rm -f .coverage .coverage.* coverage.xml

# Move test fixtures to proper location
mkdir -p tests/fixtures/orcaflex
git mv benchmarks/legacy_projects/* tests/fixtures/orcaflex/

# Untrack generated outputs
git rm -r --cached benchmarks/reports benchmarks/results

# Add to .gitignore
echo "benchmarks/reports/" >> .gitignore
echo "benchmarks/results/" >> .gitignore

root/
├── agents/
├── .agents/
├── agent_configs/
└── .agent-os/

.claude/
└── agents/
    ├── core/
    ├── devops/
    └── specialized/

# Find scattered agent directories
find . -maxdepth 2 -type d -name "*agent*"

# Move to consolidated location
git mv agents/* .claude/agents/ 2>/dev/null
git mv .agents/* .claude/agents/ 2>/dev/null
rm -rf agents .agents agent_configs

# Create runtime directory
mkdir -p .claude-flow/state
mkdir -p .claude-flow/cache

# Move runtime files (don't use git mv - these are untracked)
mv .coordination/* .claude-flow/state/ 2>/dev/null
mv .session/* .claude-flow/state/ 2>/dev/null

mkdir -p examples/prototypes
git mv prototype_*.py examples/prototypes/
git mv experimental/ examples/prototypes/

mkdir -p tests/outputs
mv tests/*.html tests/outputs/
mv tests/*.json tests/outputs/
mv tests/test_results/ tests/outputs/

# Archive completed plan (check status: completed in YAML frontmatter)
mkdir -p specs/archive
git mv specs/modules/<completed-plan>.md specs/archive/

# List all hidden directories with sizes
du -sh .*/ 2>/dev/null | grep -v "^\./\.git"

# Find dead symlinks in hidden folders
find .agent-runtime -type l ! -exec test -e {} \; -print 2>/dev/null

# Count files in each hidden directory
for dir in .claude .agent-os .ai .common .specify; do
  if [ -d "$dir" ]; then
    count=$(find "$dir" -type f | wc -l)
    echo "$dir: $count files"
  fi
done

# Remove dead symlink directories
rm -rf .agent-runtime/

# Remove stale template directories
rm -rf .specify/

# Remove orphaned utilities (after relocating useful scripts)
rm -rf .common/

# Consolidate .agent-os to .claude
git mv .agent-os/agents/* .claude/agents/ 2>/dev/null
git mv .agent-os/skills/* .claude/skills/ 2>/dev/null
git mv .agent-os/docs/* .claude/docs/ 2>/dev/null
rm -rf .agent-os/

# Consolidate .ai to .claude
git mv .ai/config/* .claude/config/ 2>/dev/null
git mv .ai/prompts/* .claude/prompts/ 2>/dev/null
rm -rf .ai/

# Rename conflicting files before merge
mv .agent-os/README.md .agent-os/README-legacy.md

# Create legacy subdirectory for scripts
mkdir -p .claude/commands/legacy-scripts
git mv .agent-os/commands/* .claude/commands/legacy-scripts/

# Preserve unique historical content
git mv .agent-os/implementation-history/ .claude/docs/implementation-history/

# Find and remove exact duplicates (verify first)
md5sum .claude/agents/*.md .agent-os/agents/*.md | sort | uniq -w32 -d

# Count tracked files in each hidden folder
for dir in .claude .agent-os .ai; do
  count=$(git ls-files "$dir" 2>/dev/null | wc -l)
  echo "$dir: $count files"
done

# Count all files (tracked + untracked)
for dir in .claude .agent-os .ai .common .specify; do
  if [ -d "$dir" ]; then
    tracked=$(git ls-files "$dir" 2>/dev/null | wc -l)
    total=$(find "$dir" -type f | wc -l)
    echo "$dir: $tracked tracked, $total total"
  fi
done

# Before/after comparison
echo "=== Before Consolidation ===" > consolidation-log.txt
for dir in .claude .agent-os .ai; do
  count=$(git ls-files "$dir" 2>/dev/null | wc -l)
  echo "$dir: $count files" >> consolidation-log.txt
done

# Verify no files were lost
expected_count=150  # Set to sum of source folders
actual_count=$(git ls-files .claude | wc -l)
echo "Expected: $expected_count, Actual: $actual_count"

# List any untracked files that might have been missed
git status --porcelain | grep "^??" | grep -E "^\?\? \.(claude|agent-os|ai)/"

# All untracked files
git status --porcelain | grep "^??"

# Untracked files with size
git status --porcelain | grep "^??" | cut -c4- | xargs -I {} sh -c 'du -h "{}" 2>/dev/null'

# Files larger than 1MB
find . -type f -size +1M -exec ls -lh {} \;

# Files larger than 10MB
find . -type f -size +10M -exec ls -lh {} \;

# Largest files in repo
find . -type f -exec du -h {} + 2>/dev/null | sort -rh | head -20

# Find duplicate markdown files in agent directories
find . -name "*.md" -path "*/agents/*" -type f

# Find files with same name
find . -type f -name "*.py" | xargs -I {} basename {} | sort | uniq -d

# Find duplicate by content (requires md5sum)
find . -type f -exec md5sum {} + | sort | uniq -w32 -d

# List all hidden directories
find . -maxdepth 1 -type d -name ".*" | grep -v "^\./\.git$"

# Hidden directories with sizes
du -sh .*/

# Remove tracked file
git rm path/to/file

# Remove tracked directory
git rm -r path/to/directory

# Remove from git but keep local copy
git rm --cached path/to/file

# Remove untracked file
rm path/to/file

# Remove untracked directory
rm -rf path/to/directory

# Interactive removal (safer)
rm -i path/to/file

# Preview what would be deleted
git clean -n -d

# Preview including ignored files
git clean -n -d -x

# Build artifacts
__pycache__/
*.py[cod]
*$py.class
*.egg-info/
*.egg
build/
dist/
.eggs/

# Test artifacts
.pytest_cache/
.coverage
.coverage.*
htmlcov/
coverage.xml
*.cover

# IDE
.idea/
.vscode/
*.code-workspace
.spyproject/

# Logs
*.log
*LogFile.txt

# Temp files
*.tmp
*.bak
*.swp
*~
.temp/
cache/

# Runtime data (claude-flow)
.claude-flow/
.coordination/
.session/

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

# Test outputs
tests/outputs/
tests/*.html
tests/*.json

# Large binary files
*.sim
*.dat
*.bin

# Delete legacy config folders
rm -rf .drcode/
rm -rf .benchmarks/

# Consolidate slash-commands to docs
mkdir -p .claude/docs/commands
git mv .slash-commands/* .claude/docs/commands/ 2>/dev/null
rm -rf .slash-commands/

# Consolidate git-commands to scripts
mkdir -p scripts/git
git mv .git-commands/* scripts/git/ 2>/dev/null
rm -rf .git-commands/

# Verify cleanup
ls -la .* 2>/dev/null | grep "^d"

## Repository Structure

project/
├── .claude/              # AI configuration and documentation
│   ├── agents/           # Agent definitions
│   ├── docs/             # Reference documentation
│   ├── skills/           # Skill definitions
│   └── settings.json     # Claude Code settings
├── .githooks/            # Git hooks
├── scripts/              # Utility scripts
│   └── git/              # Git-related scripts
├── src/<pkg>/modules/    # Source modules (5-layer architecture)
├── tests/modules/        # Test modules
├── specs/modules/        # Specification modules
├── docs/modules/         # Documentation modules
└── examples/modules/     # Example modules