docs: refresh architecture documentation

[EItanya]

Summary

• document the current v2 resource ownership and end-to-end architecture
• add focused guides for compilation, runtime lifecycle, A2A persistence, checkpoints and forks, and MCP
• clarify implemented versus deferred subagent and HITL behavior
• add Mermaid diagrams for the major control and data flows

Validation

• git diff --check
• verified local documentation links