Sync skill registry across CLI, runtime, and store layers

[humandebri]

Summary

• Add end-to-end skill registry synchronization across the CLI, runtime, client, and store layers.
• Update canister interfaces, migrations, tests, and benchmark helpers to cover the new registry flow.
• Refresh extension, plugin, and documentation assets to match the new behavior.

Testing

• Added and updated unit, integration, and property-based tests for skill registry, store sync, and VFS behavior.
• Updated smoke and benchmark coverage for local archive/restore and scale scenarios.
• Not run (not requested)