docs: comprehensive documentation rewrite

[dimakis]

Summary

• Rewrites README with accurate module tables, full API summary table, documentation index, updated architecture diagram, and new features (multi-model reasoning, desktop mode, APNs)
• Creates seven new dedicated documentation files covering all major systems in depth

New Documentation

Document	Description
docs/architecture.md	Module structure, data flow diagrams, request flow walkthrough, session lifecycle state machine, event store, permission system, observability stack, design decisions
docs/api-reference.md	Complete REST API reference -- every endpoint with request/response JSON schemas, query parameters, error codes. Covers auth, sessions, chat (WS + REST), tasks, files, skills, calendar, todos, workload, inbox, signals, push notifications
docs/v2-protocol.md	WebSocket streaming protocol guide -- handshake, reconnection with seq replay, session management, full block lifecycle (message_start/block_start/delta/end/tool_result/message_end), deferred message_end, subagent nesting, SSE fallback
docs/skills.md	Skills system user guide -- bundled skills table, custom skill authoring with frontmatter format, discovery scopes and precedence, tool restriction ceiling, API reference
docs/task-board.md	Task orchestration guide -- task tree hierarchy, status cascade, DFS ordering, spec mode, orchestrator state machine, agent MCP tools, task context injection, workflow templates with gate configs, full REST API
docs/session-isolation.md	Worktree isolation guide -- multi-repo setup, write enforcement by client, system prompt injection, external hooks (Claude Code/Cursor), cleanup and dirty worktree handling, session index, troubleshooting
docs/packages.md	npm workspace package reference -- full type definitions and API for @mitzo/protocol (message types, schemas, event store), @mitzo/harness (session registry, connection registry, permission handler, model providers, reasoning orchestrators), @mitzo/client (MitzoConnection, Zustand store with 12 slices, protocol parser, API client, React hooks)

Test plan

• Verify all internal doc links resolve (e.g., docs/v2-protocol.md from README)
• Verify design doc references in architecture.md and task-board.md are correct
• Spot-check API endpoint descriptions against actual route implementations
• Confirm no hardcoded test counts or stale metrics

🤖 Generated with Claude Code