[Bug]: "install_ai_skills" creates spurious skills from non-speckit agent files when using "--ai copilot --ai-skills" #1858

Bug Description

install_ai_skills creates spurious skills from non-speckit agent files when using --ai copilot --ai-skills

Summary

When running specify init --here --ai copilot --ai-skills in a project that already has custom (non-speckit) agent files in .github/agents/, the install_ai_skills() function treats every .md file in that directory as a spec-kit command template - not just the speckit.* ones. This produces unexpected skill directories for user-authored agents that have nothing to do with spec-kit.

Root Cause

In src/specify_cli/__init__.py, AGENT_CONFIG defines the copilot entry as:

"copilot": {
    "folder": ".github/",
    "commands_subdir": "agents",   # ← shared user directory
}

For every other agent type, commands_subdir points to a dedicated directory (e.g. "commands"). For copilot, it points to .github/agents/ - the same directory that holds both spec-kit command agents and user-authored agents.

install_ai_skills() then performs an unfiltered glob:

templates_dir = project_path / agent_folder / commands_subdir   # resolves to .github/agents/
command_files = sorted(templates_dir.glob("*.md"))              # picks up ALL .md files

Every .md file in .github/agents/ becomes a skill candidate, regardless of whether it is a spec-kit command or a user-authored agent.

Steps to Reproduce

Steps to Reproduce

1. Create a fresh spec-kit copilot project:

   mkdir /tmp/repro && cd /tmp/repro
   specify init --here --ai copilot --ai-skills

2. Add a custom (non-speckit) agent file alongside the generated speckit ones:

   cat > .github/agents/my-custom-agent.agent.md << 'EOF'
   ---
   name: my-custom-agent
   description: "A user-authored agent unrelated to spec-kit"
   ---
   You are a custom agent.
   EOF

3. Simulate a re-init / upgrade

   specify init --here --ai copilot --ai-skills

4. Inspect the generated skills directory:

   ls .github/skills/

Expected Behavior

Only speckit-analyze/, speckit-checklist/, etc. (the standard spec-kit commands).

Actual Behavior

Also creates speckit-my-custom-agent.agent/SKILL.md - a skill wrapper for the user's custom agent, with author: github-spec-kit falsely attributed in the frontmatter.

Specify CLI Version

0.3.0

AI Agent

Claude Code

Operating System

Ubuntu (WSL2) / Windows 11

Python Version

3.12.3

Error Logs

Additional Context