feat(cli): publish MCP-first interface cleanup

[orga-agent]

Summary

• retire CLI content and section mutation commands in favor of the structured MCP interface
• add typed topic/entity discovery tools and hide internal note status from public DTOs
• bump the daemon RPC protocol to v3 and update CLI/MCP guidance and skill installation

Verification

• cargo test --workspace
• cargo clippy --workspace --all-targets --all-features -- -D warnings
• cargo fmt --all --check
• cargo deny check