refactor(skills): simplify loading to managed + profile sources

- Remove bundled, extraDirs, and plugin skill sources
- Skills now load from only two sources:
  1. managed (~/.super-multica/skills/) - global skills
  2. profile (~/.super-multica/agent-profiles/<id>/skills/) - profile-specific
- Add initializeManagedSkills() to copy bundled skills on first run
- Delete plugin.ts (multica.plugin.json discovery)
- Update documentation and tests

This simplifies the architecture by treating bundled skills as
managed skills that are initialized once, rather than maintaining
multiple loading sources with complex precedence.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

README.md

@@ -157,12 +157,11 @@ Skills are modular capabilities that extend agent functionality through `SKILL.m
 
 ### Key Features
 
-- **Multi-source loading** - Bundled, user-installed, plugin-based, and profile-specific skills
+- **Two-source loading** - Global skills (`~/.super-multica/skills/`) and profile-specific skills
 - **GitHub installation** - `pnpm skills:cli add owner/repo` to install from GitHub
 - **Slash command invocation** - `/skill-name args` in interactive mode
 - **Eligibility filtering** - Auto-filter by platform, binaries, and environment
 - **Hot reload** - File watcher for development
-- **Plugin system** - Auto-discover skills from npm packages with `multica.plugin.json`
 
 ### Quick Start