Complete documentation refresh covering:
- Version detection via CLI binary mtime (not package.json)
- Multi-Agent Support section with token authentication for claude/codex/gemini
- Directory creation approval flow for session spawning
- HTTP Control Server endpoints with Fastify + Zod schemas
- State persistence fields including startedWithCliMtimeMs
- Integration Testing section with test environment and key scenarios
- Typed shutdown sources (hapi-app, hapi-cli, os-signal, exception)
- MachineMetadata with new happyLibDir field
- WebSocket communication patterns and RPC methods
- Machine sync architecture with separated metadata and daemon state
Replaces CLAUDE.md with structured daemon documentation.
