Fix/clerk oauth domain consistency

[mgoldsborough]

Updates to support v0.2.0 of nimbletools.

• Support for core registry/server schemas and registry.nimbletools.ai
• Consolidate authentication to use NimbleBrain bearer tokens instead of managing separate Clerk and workspace tokens
• Add token exchange flow to convert Clerk ID tokens to NimbleBrain API tokens
• Implement registry creation command and migrate registry client from management to dedicated API
• Add workspace token management and update MCP commands to use correct token scopes
• Improve CLI verification scripts and add local development setup tools
• Update documentation and remove unnecessary dependencies (globals)