fix(cli): resolve CLI bugs and add comprehensive e2e test suite

[m2papierz]

Summary

Fixes four CLI bugs discovered during test development and adds a comprehensive end-to-end test suite for the devqubit public API and CLI.

Bug fixes:

• baseline set passed 3 arguments to set_baseline() instead of 2
• storage gc referenced non-existent GCStats.objects_total attribute
• storage prune treated PruneStats dataclass as a dict
• search passed unsupported project kwarg to search_runs()

Type of change

• Bug fix
• New feature
• Refactor (no user-facing change)
• Docs only
• CI/build tooling
• Breaking change

Checklist

• I ran lint locally (uv run pre-commit run --all-files)
• I ran tests locally (uv run pytest)
• I added/updated tests for behavior changes
• I updated docs/README/examples if needed
• If I changed dependencies, I updated uv.lock (uv lock) and committed it
• I considered backward compatibility and security impact