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fix(genkit-cli/mcp): get RuntimeManager lazily for MCP
This PR will defer manager creation to the listFlows/ lookupTrace tools, which means that the .genkit folder is not created unless these tools are called (which in turn need the runtime present).
Checklist (if applicable):
- [x] PR title is following https://www.conventionalcommits.org/en/v1.0.0/
- [x] Tested (manually)