Update cleanup flow and GitHub workflows for npm release reliability

[TrueNine]

Summary

• fix composite GitHub actions to accept npm auth tokens via inputs instead of direct secrets.* access
• update release and PR workflows, cross-compile setup, and docs workflow wiring
• refine cleanup and protected deletion behavior in the SDK and native cleanup path
• sync package metadata and workspace configuration across CLI, SDK, MCP, GUI, docs, and libraries

Testing

• Not run (not requested)