Thoughts Directory Management

Manage the thoughts/ directory system for organizing research, plans, and notes with efficient searchable hardlinks.

When to use this Skill

Use this Skill automatically in these situations:

• After creating research documents in thoughts/shared/research/
• After creating implementation plans in thoughts/shared/plans/
• After modifying any markdown files in thoughts/
• When gathering metadata for document frontmatter (git commit, branch, author)
• When initializing a new project that needs thoughts/ structure

Available operations

Initialize thoughts directory

Creates the complete thoughts/ directory structure in the current project.

When to use:

• First time setting up thoughts/ in a new project
• When thoughts/ directory doesn't exist

Command:

bash ${CLAUDE_PLUGIN_ROOT}/skills/thoughts-management/scripts/thoughts-init

What it does:

• Creates directory structure: {username}/, shared/, searchable/
• Generates .gitignore for searchable/ directory
• Creates initial README.md
• Runs initial sync to create hardlinks

Sync searchable directory

Synchronizes hardlinks in thoughts/searchable/ for efficient grep operations.

When to use:

• After creating new markdown files in thoughts/
• After modifying existing markdown files in thoughts/
• After completing a /stepwise-dev:research_codebase command
• After completing a /stepwise-dev:create_plan command
• After completing a /stepwise-dev:iterate_plan command

Command:

bash ${CLAUDE_PLUGIN_ROOT}/skills/thoughts-management/scripts/thoughts-sync

What it does:

• Creates hardlinks for all .md files in searchable/
• Removes orphaned links (when source files are deleted)
• Maintains flat searchable/ structure for fast grep
• Reports statistics (added, removed, skipped)

Important: Always run this after creating or modifying documents in thoughts/

Generate metadata

Generates git and project metadata for document frontmatter.

When to use:

• Before creating research document frontmatter
• Before creating implementation plan frontmatter
• When you need current git commit, branch, repository info
• When you need timestamp information

Command:

bash ${CLAUDE_PLUGIN_ROOT}/skills/thoughts-management/scripts/thoughts-metadata

Output format:

Current Date/Time (TZ): 2025-01-12 14:30:45 PST
ISO DateTime: 2025-01-12T14:30:45-0800
Date Short: 2025-01-12
Current Git Commit Hash: abc123def456
Current Branch Name: main
Repository Name: my-project
Git User: John Doe
Git Email: john@example.com
Timestamp For Filename: 2025-01-12_14-30-45

Use this metadata to populate:

• Research document frontmatter fields
• Implementation plan frontmatter fields
• Any document requiring git context

Workflow integration

Research workflow

1. Run /stepwise-dev:research_codebase command
2. Command generates research document in thoughts/shared/research/
3. Automatically run sync:

   bash ${CLAUDE_PLUGIN_ROOT}/skills/thoughts-management/scripts/thoughts-sync
   

Planning workflow

1. Run /stepwise-dev:create_plan or /stepwise-dev:iterate_plan command
2. Command generates/updates plan in thoughts/shared/plans/
3. Automatically run sync:

   bash ${CLAUDE_PLUGIN_ROOT}/skills/thoughts-management/scripts/thoughts-sync
   

Metadata collection workflow

1. Need to create document with frontmatter
2. First, gather metadata:

   bash ${CLAUDE_PLUGIN_ROOT}/skills/thoughts-management/scripts/thoughts-metadata
   

3. Use output to populate YAML frontmatter fields
4. Create the document
5. Sync after creation

Directory structure

The thoughts/ system maintains this structure:

thoughts/
├── {username}/              # Personal notes (default: nikey_es)
│   ├── tickets/            # Ticket documentation
│   └── notes/              # Personal observations
├── shared/                 # Team-shared documents
│   ├── research/          # Research documents
│   ├── plans/             # Implementation plans
│   └── prs/               # PR descriptions
└── searchable/            # Auto-generated hardlinks
    └── [hardlinks to all .md files for fast grep]

Key concepts

Hardlinks vs copies

• thoughts-sync creates hardlinks, not copies
• Same file, multiple directory entries
• No disk space duplication
• Fast grep across all documents in searchable/

Searchable directory

• Contains hardlinks to ALL .md files in thoughts/
• Flattened structure for efficient searching
• Automatically maintained by thoughts-sync
• Gitignored (generated, not source)

Path handling

• When finding files in searchable/, always document paths by removing "searchable/"
• Preserve all other subdirectories: thoughts/searchable/nikey_es/notes/X.md → thoughts/nikey_es/notes/X.md
• Never change directory structure when removing "searchable/" prefix

Best practices

1. Always sync after document creation - Keep searchable/ up to date
2. Gather metadata before writing - Populate frontmatter with real values, never placeholders
3. Run sync even for single files - Maintains consistency
4. Don't edit files in searchable/ - Edit in original locations only
5. Let the scripts handle hardlinks - Don't create them manually

Configuration

Set custom username (optional):

export THOUGHTS_USER=your_name

Default username: nikey_es

Troubleshooting

Sync reports orphaned links

Cause: Files were deleted from thoughts/ but hardlinks remain in searchable/

Solution: The script automatically cleans them up. No action needed.

Metadata returns "no-branch" or "no-commit"

Cause: Not in a git repository or git not available

Solution: Ensure you're in a git repository. For testing, the script provides fallback values.

Permission denied on scripts

Cause: Scripts are not executable

Solution: Run chmod:

chmod +x ${CLAUDE_PLUGIN_ROOT}/skills/thoughts-management/scripts/*

Script reference

All scripts are located in: ${CLAUDE_PLUGIN_ROOT}/skills/thoughts-management/scripts/

Script	Purpose	When to use
thoughts-init	Initialize directory structure	Once per project
thoughts-sync	Synchronize hardlinks	After every document change
thoughts-metadata	Generate git metadata	Before creating frontmatter

Integration with commands

The following slash commands automatically use this Skill:

• /stepwise-dev:research_codebase - Uses thoughts-metadata and thoughts-sync
• /stepwise-dev:create_plan - Uses thoughts-metadata and thoughts-sync
• /stepwise-dev:iterate_plan - Uses thoughts-sync
• /stepwise-dev:implement_plan - Uses thoughts-sync
• /stepwise-dev:validate_plan - Uses thoughts-sync

These commands will automatically invoke the appropriate scripts when needed.