docs: Add Phase 2 core package documentation (Execution, Config, Runtime, Security)

Comprehensive documentation for 7 critical packages covering execution engine,
configuration management, runtime infrastructure, and security layers.

Package Documentation Added:
- pkg/execution - Complete task execution engine API (Docker sandboxing, image selection)
- pkg/config - Configuration management (80+ env vars, dynamic assignments, SIGHUP reload)
- internal/runtime - Shared P2P runtime (initialization, lifecycle, agent mode)
- pkg/dht - Distributed hash table (LibP2P DHT, encrypted storage, bootstrap)
- pkg/crypto - Cryptography (age encryption, key derivation, secure random)
- pkg/ucxl - UCXL validation (decision publishing, content addressing, immutable audit)
- pkg/shhh - Secrets management (sentinel, pattern matching, redaction, audit logging)

Documentation Statistics (Phase 2):
- 7 package files created (~12,000 lines total)
- Complete API reference for all exported symbols
- Line-by-line source code analysis
- 30+ usage examples across packages
- Implementation status tracking (Production/Beta/Alpha/TODO)
- Cross-references to 20+ related documents

Key Features Documented:
- Docker Exec API usage (not SSH) for sandboxed execution
- 4-tier language detection priority system
- RuntimeConfig vs static Config with merge semantics
- SIGHUP signal handling for dynamic reconfiguration
- Graceful shutdown with dependency ordering
- Age encryption integration (filippo.io/age)
- DHT cache management and cleanup
- UCXL address format (ucxl://) and decision schema
- SHHH pattern matching and severity levels
- Bootstrap peer priority (assignment > config > env)
- Join stagger for thundering herd prevention

Progress Tracking:
- PROGRESS.md added with detailed completion status
- Phase 1: 5 files complete (Foundation)
- Phase 2: 7 files complete (Core Packages)
- Total: 12 files, ~16,000 lines documented
- Overall: 15% complete (12/62 planned files)

Next Phase: Coordination & AI packages (pkg/slurp, pkg/election, pkg/ai, pkg/providers)

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

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

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