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docs: Add comprehensive documentation foundation (Phase 1: Architecture & Commands)

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Created complete documentation infrastructure with master index and detailed
command-line tool documentation.

Documentation Structure:
- docs/comprehensive/README.md - Master index with navigation
- docs/comprehensive/architecture/README.md - System architecture overview
- docs/comprehensive/commands/chorus-agent.md - Autonomous agent binary (✅ Production)
- docs/comprehensive/commands/chorus-hap.md - Human Agent Portal (🔶 Beta)
- docs/comprehensive/commands/chorus.md - Deprecated wrapper (⚠️ Deprecated)

Coverage Statistics:
- 3 command binaries fully documented (3,056 lines, ~14,500 words)
- Complete source code analysis with line numbers
- Configuration reference for all environment variables
- Runtime behavior and execution flows
- P2P networking details
- Health checks and monitoring
- Example deployments (local, Docker, Swarm)
- Troubleshooting guides
- Cross-references between docs

Key Features Documented:
- Container-first architecture
- P2P mesh networking
- Democratic leader election
- Docker sandbox execution
- HMMM collaborative reasoning
- UCXL decision publishing
- DHT encrypted storage
- Multi-layer security
- Human-agent collaboration

Implementation Status Tracking:
- ✅ Production features marked
- 🔶 Beta features identified
- ⏳ Stubbed components noted
- ⚠️ Deprecated code flagged

Next Phase: Package documentation (30+ packages in pkg/)

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

Co-Authored-By: Claude <noreply@anthropic.com>
This commit is contained in:
anthonyrawlins
2025-09-30 13:49:46 +10:00
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