Skill Manager

Unified CLI for managing AI skills across all IDEs.

CRITICAL: Global vs Project Skills

ALWAYS confirm scope before any operation. Default assumptions cause errors.

Mandatory Confirmation

Before install, create, or sync, ALWAYS ask user:

"Should this skill be installed globally (~/.ai-skills/) or for this project only (./.ai-skills/)?"

Default behavior:

• If user says "project" or "local" → use ./.ai-skills/ in current working directory
• If user says "global" → use ~/.ai-skills/
• If unclear → ASK, do not assume

Mandatory Rules

1. Git tracking: When creating or editing skills, ensure all changes are tracked by Git within the project repository.
2. Project-first: All skill files MUST be created within the current repository only. Only sync to global (~/.ai-skills/ → ~/.claude/skills/) after testing AND explicit user request. Never auto-sync to global.

Common Mistake to Avoid

WRONG: User says "save to project" but agent syncs to ~/.claude/skills/ RIGHT: User says "save to project" → save to ./.cursor/skills/ or ./.ai-skills/ in CWD

WRONG: Agent creates skill and immediately syncs to ~/.claude/skills/ RIGHT: Agent creates skill in project repo → tests it → user explicitly says "sync to global" → then sync

Skill Guidelines Reference

When creating or modifying skills: references/skill-creator/SKILL.md

Important Paths

Search Workflow (MUST FOLLOW)

When user asks to search/find skills, follow this fallback chain in order:

Step 1: Check Local Installed Skills

# Check global
ls ~/.ai-skills/
# Check project
ls ./.ai-skills/

If a matching skill is already installed, inform user and stop.

Step 2: Search Custom Sources

Check the Custom Skill Sources table below. Match user's query against the listed categories and skill names.

• If user asks about biology, bioinformatics, genomics, drug discovery → search K-Dense-AI/claude-scientific-skills
• Browse the repo to find matching skills, read their SKILL.md for details

Step 3: Search skills.sh

npx skills search "<query>"

Or browse https://skills.sh for the leaderboard.

Step 4: Search GitHub

If nothing found above, search GitHub for skill repositories:

• Search query: <topic> claude skill SKILL.md
• Look for repos with proper skill structure (SKILL.md with frontmatter)

Search Result Format

Always present results to user in this format:

Found: <skill-name>
Source: <skills.sh | Custom: K-Dense-AI | GitHub: owner/repo>
Description: <from SKILL.md description>
Install: <command>

Quick Reference

Custom Skill Sources

Beyond skills.sh, these curated repositories contain high-quality skills:

Scientific Skills (Biology Focus)

Repository: https://github.com/K-Dense-AI/claude-scientific-skills

Genomics & Sequencing: alphafold-database, biopython, scanpy, pysam, ensembl-database, cellxgene-census, scvi-tools, pydeseq2

Drug Discovery: rdkit, chembl-database, deepchem, pubchem-database, drugbank-database, diffdock

Clinical/Health: clinical-decision-support, pyhealth, clinicaltrials-database, pydicom, pathml

Lab Automation: opentrons-integration, benchling-integration, lamindb, pylabrobot

Install from this source:

# Clone the scientific skills repo
git clone https://github.com/K-Dense-AI/claude-scientific-skills.git /tmp/scientific-skills

# Install a specific skill (e.g., biopython)
# Global:
cp -r /tmp/scientific-skills/scientific-skills/biopython ~/.ai-skills/
# Project:
cp -r /tmp/scientific-skills/scientific-skills/biopython ./.ai-skills/

# Then sync to IDE
cp -r ~/.ai-skills/biopython ~/.claude/skills/

Installing Skills (via skills.sh)

Search Skills

Browse the leaderboard at https://skills.sh to find community skills.

Install from skills.sh

# Install a skill (goes to current directory by default)
npx skills add <owner>/<skill-name>

# Examples:
npx skills add anthropics/skills/docx
npx skills add vercel-labs/skills/find-skills

Post-Install: Choose Scope

After npx skills add, the skill is downloaded. Then:

1. For Global: Move to ~/.ai-skills/<skill-name>/
2. For Project: Move to ./.ai-skills/<skill-name>/

Then sync to appropriate IDE paths.

Manual Install (from GitHub)

# Clone skill repo
git clone <github-url> /tmp/skill-temp

# Copy to appropriate scope
# Global:
cp -r /tmp/skill-temp/<skill-name> ~/.ai-skills/
# Project:
cp -r /tmp/skill-temp/<skill-name> ./.ai-skills/

Sync to IDEs

After installing to SSOT, sync to IDE-specific paths:

# Global sync (from ~/.ai-skills/ to ~/.claude/skills/, ~/.cursor/skills/, etc.)
cp -r ~/.ai-skills/<skill-name> ~/.claude/skills/
cp -r ~/.ai-skills/<skill-name> ~/.cursor/skills/

# Project sync (from ./.ai-skills/ to ./.cursor/skills/)
cp -r ./.ai-skills/<skill-name> ./.cursor/skills/

Creating Skills

Follow references/skill-creator/SKILL.md for:

• SKILL.md structure (frontmatter + body)
• Progressive disclosure pattern
• Resource organization (scripts/, references/, assets/)

Quick Create Template

---
name: my-skill
description: >-
  What the skill does. When to use it (triggers, contexts, examples).
---

# My Skill

Instructions for using the skill...

Scope Flags (Legacy Scripts)

If using legacy Python scripts:

• -g, --global: Global scope (~/.ai-skills/)
• -l, --local: Project scope (./.ai-skills/)

Validation Checklist

• SKILL.md exists with valid YAML frontmatter
• name and description fields present
• Description includes trigger phrases
• No extraneous files (README.md, CHANGELOG.md, etc.)
• Resources in correct folders (scripts/, references/, assets/)

Troubleshooting