Deleting a crate's structural index removes entities other crates share #35

Problem

An entity's id is its primary key, so when several crates contain the same entity (for example https://github.com/Language-Research-Technology/crate-o), only the first crate to be indexed stores it. StructuralIndexer.index sets rootCollection to that crate, and every later crate's prisma.entity.create fails with a duplicate-key error, which is logged as "Error indexing entity" and skipped (src/indexer/structural.ts).

StructuralIndexer.delete(crateId) deletes by rootCollection, so deleting the first crate's index removes the shared entity (and its file) for every crate. The other crates have no copy until one of them is reindexed.

This predates the admin pages, but the admin pages' Delete action (#32) makes it easy to hit.

Reproduce

1. Index two crates that both contain the same entity.
2. Delete the index of whichever was indexed first.
3. The entity is gone from the structural index, though the second crate still references it.

Expected

Deleting one crate's index leaves entities that other indexed crates still contain.

Notes

• Entities counted twice show up as duplicate-key errors in the logs on every full index run (seen in CI on PR feat!: admin pages served by the API, with sign-in #33).
• Possible directions: track which crates contain each entity (a join table) and delete an entity only when no crate is left; or reindex the remaining owners after a delete. Needs a design decision.