refactor: migrate to clean architecture with src/ layout

## Migration Summary
- Moved from flat `superclaude/` to `src/superclaude/` (PEP 517/518)
- Deleted old structure (119 files removed)
- Added new structure with clean architecture layers

## Project Structure Changes
- OLD: `superclaude/{agents,commands,modes,framework}/`
- NEW: `src/superclaude/{cli,execution,pm_agent}/`

## Build System Updates
- Switched: setuptools → hatchling (modern, PEP 517)
- Updated: pyproject.toml with proper entry points
- Added: pytest plugin auto-discovery
- Version: 4.1.6 → 0.4.0 (clean slate)

## Makefile Enhancements
- Removed: `superclaude install` calls (deprecated)
- Added: `make verify` - Phase 1 installation verification
- Added: `make test-plugin` - pytest plugin loading test
- Added: `make doctor` - health check command

## Documentation Added
- docs/architecture/ - 7 architecture docs
- docs/research/python_src_layout_research_20251021.md
- docs/PR_STRATEGY.md

## Migration Phases
- Phase 1: Core installation ✅ (this commit)
- Phase 2: Lazy loading + Skills system (next)
- Phase 3: PM Agent meta-layer (future)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

src/superclaude/__init__.py

@@ -0,0 +1,23 @@
+"""
+SuperClaude Framework
+
+AI-enhanced development framework for Claude Code.
+Provides pytest plugin for enhanced testing and optional skills system.
+"""
+
+__version__ = "0.4.0"
+__author__ = "Kazuki Nakai"
+
+# Expose main components
+from .pm_agent.confidence import ConfidenceChecker
+from .pm_agent.self_check import SelfCheckProtocol
+from .pm_agent.reflexion import ReflexionPattern
+from .pm_agent.token_budget import TokenBudgetManager
+
+__all__ = [
+    "ConfidenceChecker",
+    "SelfCheckProtocol",
+    "ReflexionPattern",
+    "TokenBudgetManager",
+    "__version__",
+]