Refactor CLI packaging and update docs for the sdk-first release flow

[TrueNine]

Summary

• Refactor the CLI runtime, command pipeline, and factories to align the public CLI shell with the sdk-first architecture
• Update Rust and npm packaging, release workflow, and distribution sync scripts for the CLI publish flow
• Refresh docs, README, and security guidance to match the current install, plugin, and troubleshooting behavior
• Expand test coverage across CLI runtime, command behavior, cleanup protection, and version sync paths

Testing

• Not run (not requested)