Rebuild missing Cell Annotation manifests from on-disk checkpoint artifacts

[Copilot]

This follow-up continues the Cell Annotation workflow scaffolding from the previous PR by replacing the placeholder manifest rebuild path. Dataset stores with checkpoint artifacts but no manifest.json can now recover their manifest state directly from disk.

• Manifest rebuild

  • Replaced the stubbed Manifest.rebuild_from_disk() implementation with a filesystem scan of:
    • checkpoints/*.json
    • matching thumbnails/*
    • matching selections/*
  • Ignores partial artifacts during rebuild.
  • Normalizes each entry to include a stable id and an artifacts map with repository-relative paths.

• Startup recovery

  • Updated CellAnnotationPlugin.on_dataset_opened() to rebuild the manifest automatically when the dataset store exists but manifest.json is missing.
  • Preserves the existing load path when a persisted manifest is already present.

• Focused coverage

  • Replaced the old stub-oriented manifest test with coverage for:
    • checkpoint/thumbnails/selections discovery
    • partial-file exclusion
    • atomic persistence of rebuilt manifest data
    • plugin startup recovery when only checkpoint metadata exists

Example rebuilt entry shape:

{
    "id": "abc123",
    "parents": ["root"],
    "op": "save",
    "artifacts": {
        "checkpoint": "checkpoints/abc123.json",
        "thumbnail": "thumbnails/abc123.png",
        "selection": "selections/abc123.parquet",
    },
}

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