Update opencloning-linkml to add migration to remove output field which was incorrectly set in the frontend in UploadedFileSource

[manulera]

closes #372

This is pending a pydna release to be possible to be released in pypi (has pydna as a git dependency), but I am going to go through because it fixes a bug.

The tests are failing because wekwikgene is down

---

Note

Upgrade opencloning-linkml to 0.4.6, source pydna from a Git ref, update a test fixture, and refresh the lockfile with transitive changes.

• Dependencies:
  • Bump opencloning-linkml to 0.4.6.
  • Switch pydna to Git source pydna-group/pydna@change-opencloning-linkml-dependency.
  • Regenerate poetry.lock with widespread transitive updates and markers.
• Tests/Fixtures:
  • Update schema_version to 0.4.6 in tests/test_files/homologous_recombination.json.

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