SIMSBIOHUB-1060i: Integrate staged reconciliation into tarball ingestion

[mauberti-bc]

Links to Jira Tickets

• https://apps.nrs.gov.bc.ca/int/jira/browse/SIMSBIOHUB-1060

Description of Changes

• Wires the upload ingestion pipeline into the new staged reconciliation jobs after raw feature ingestion completes.
• Adds the end-to-end flow for reconciling staged upload features, promoting changed features, and indexing feature properties.
• Updates queue publishers and workers so reconciliation, promotion, indexing, closure recompute, and security screening run in the intended order.
• Keeps approval separate from ingestion, with approval only allowed after the upload reaches indexed.
• Updates status transitions so downstream jobs do not run before their prerequisite ingestion steps are complete.

Testing Notes

• Download the tarball attached to the Jira ticket and upload it to a test submission.
• Confirm the upload progresses through the new ingestion pipeline: uploaded → ingesting → ingested → reconciling → reconciled → promoting → promoted → indexing → indexed.
• Confirm reconciliation completes without conflicts and reports the expected new, unchanged, superseded, and conflict counts.
• Verify staged features are not active or visible in the submission before the upload is approved.
• Approve the indexed upload and verify its new and superseding features become active.
• Confirm unchanged features are not duplicated and superseded features are ended correctly.
• Verify feature closure is recomputed after approval and parent-child feature relationships remain correct.
• Confirm the security-processing job runs independently and does not block ingestion, indexing, or approval.
• Re-submit or retry a completed job and confirm processing is idempotent, with no duplicate features or status transitions.
• Revoke the approval and confirm features owned by that upload are ended and the appropriate prior features are restored.

[github-actions]

OpenShift URLs for the PR Deployment:

• App Route: https://biohub-platform-app-522-a0ec71-dev.apps.silver.devops.gov.bc.ca/
• API Route: https://biohub-platform-api-522-a0ec71-dev.apps.silver.devops.gov.bc.ca/
• Pods: https://console.apps.silver.devops.gov.bc.ca/k8s/ns/a0ec71-dev/pods?name=522
• Helm Release: https://console.apps.silver.devops.gov.bc.ca/helm-releases/ns/a0ec71-dev/release/pr-522

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud