v0.6.0: Restructure repository with .claude/ directory

The Problem:
Users reported issues with PAI not working correctly because the repository
structure didn't match the actual working system. The real PAI system expects
all infrastructure to live in ~/.claude/, but the repo had everything at root
level. This caused confusion and compatibility problems.

The Solution:
- Created .claude/ directory at repository root
- Moved ALL PAI infrastructure into .claude/ (agents, commands, documentation,
  hooks, skills, voice-server, etc.)
- Kept GitHub infrastructure at root (README, LICENSE, .gitignore, .github)
- Repository now serves as a true reference implementation

What Changed:
- All functional directories now in .claude/
- Updated README with v0.6.0 changelog and migration guide
- Updated documentation with structure notes
- All path references updated to reflect new structure

Why This Matters:
1. Proper Emulation: Repository accurately represents how PAI works in production
2. Easier Setup: Users see exactly how ~/.claude/ directory should be structured
3. Less Confusion: Clear separation between GitHub files and PAI infrastructure
4. Better Documentation: Structure itself serves as documentation
5. Reference Implementation: Can be copied/referenced directly for setup

🤖 Generated with Claude Code

Co-Authored-By: Claude <[email protected]>

Author: danielmiessler