[TorecLuik]

Successful shallow imports lost storage provenance because the reader expected top-level images and nested source records. Parse the actual schema-2 graph/binding contract with ShallowManifest, select the correct Image node, and preserve workflow, managed-path, receipt and ambiguity checks. Full-Zarr handling remains independent of shallow feature flags.

Partial metadata now produces an explicit WARNING in the import script's Message while keeping imported data available. Storage evidence is persisted before rendering workflow maps.

Add an administrator-only, dry-run-by-default backfill that reads existing managed evidence and records it once, refusing conflicting history. Expose an explicit storage-repair option through the existing metadata persistence adapter, retaining its backups and shared-annotation protections. The README documents both steps. Pixel arrays are never read or rewritten by repair.

Closes #41.

Validation: 293 passed, 4 existing skips across the complete separate harness, plus script compilation and git diff --check. Initial schema-2 regression run: 23 failed / 6 guards passed; the additional repair-adapter and conflicting-evidence tests also failed before their fixes. Real schema-2 fixtures cover Image/Plate bindings, both interchange profiles, invalid manifests/references, warnings, persistence order and idempotent repair. Live OMERO/ACC acceptance remains to be run after deployment.

Dependencies and merge order:

• The companion harness PR Test schema-2 storage provenance, warnings and recovery #45 into test-suite must merge first, then rerun this PR's CI. The current canonical harness uses schema 0.2 and invalid legacy shallow fixtures, so it cannot validate this fixed reader. The updated harness also passes unchanged master: 261 passed, 36 skipped, with new behavior capability-gated.
• Explicit repair refresh requires Allow explicit refresh of backfilled result storage provenance biomero#47 in the coordinated core build. Default refresh and normal imports do not invoke that new option.

Kept in draft until the canonical harness prerequisite is merged. No tests are included in the deployable branch; no release or data repair was performed.