feat: streamline scaffolding agent workflows

[vuongngo]

Summary

• move scaffolding guidance toward skill plus CLI workflows
• make scaffold server workspace context immutable instead of relying on later process.cwd changes
• clean up scaffold stdio transport on EOF, close and repeated shutdown
• add workspace-isolation and transport lifecycle coverage
• include all current toolkit working-tree updates requested for this PR

Verification

• all 8 workspace project test targets passed in the pre-commit hook
• scaffold MCP: 298 tests passed locally
• aicode-utils: 102 tests passed locally
• affected build and typecheck targets passed