transaction: bundle references are stored unresolved — urn:uuid fullUrls are not rewritten and conditional references are never resolved

[angela-helios]

Found by the #448 R4 parameter sweep (SQLite, main @ 2026-07-30), ingesting Synthea transaction bundles.

1. urn:uuid references survive into storage

Synthea bundles reference sibling entries by fullUrl (urn:uuid:<id>). After a successful transaction, the stored resources still carry the urn:

GET /Observation?_count=1 → .subject.reference == "urn:uuid:8712799b-3834-10cc-87b8-9474304f2d04"

Per the Bundle processing rules the server must rewrite references to bundle entries to the ids it assigned. Search mostly papers over it — the indexer evidently strips the prefix and the uuid happens to equal the assigned id, so Observation?patient=<id> works — but any client that reads the resource gets a dangling urn:uuid, and Observation?subject=urn:uuid:<id> (the literal in the body) matches nothing.

2. Conditional references are stored verbatim

GET /Immunization?_count=1 → .location.reference == "Location?identifier=https://github.com/synthetichealth/synthea|62163921-…"

Transaction processing is supposed to resolve conditional references against the server's data (or reject). Stored as-is they are unsearchable (Immunization?location=… can never match) and unresolvable by any client.

Both are the same subsystem (bundle reference resolution at commit); Synthea is a convenient repro because it uses both styles heavily. Practitioner/Organization-side references from the batch bundles show the same behavior.

Part of the #448 sanity pass.

[angela-helios]

Scope correction after digging in: facet 1 (urn:uuid rewriting) is a false alarm — replaying both a minimal transaction and a real Synthea bundle against a clean server shows stored references correctly rewritten to Type/id. The dangling urn:uuid resources in my report came from the #448 $bulk-submit NDJSON, which I had built by extracting raw bundle-entry resources (urns and all) — test-data artifact, not a server bug. Facet 2 (conditional references stored verbatim) is confirmed and is what the fix addresses.