Overview

In Aqua Supply Chain Security, repositories integrated through a specific GitHub organization or environment can occasionally appear under a generic "GitHub" system entry. The repository name may become unclickable, scan actions disabled, and the backend link to the correct SCM integration ID may be lost. This article describes symptoms, root cause at a high level, and recovery steps.

Symptoms

  • A repository previously tied to a named GitHub integration (for example, an organization-specific connector) appears under generic GitHub.
  • Repository row is not clickable in the Aqua UI.
  • Scan controls are disabled for the affected repository.
  • Re-adding the repository temporarily fixes the issue; the problem may recur after background synchronization.

Understanding Orphaned Repository Metadata

This behavior is consistent with orphaned repository metadata: the Aqua backend record for the repository no longer references the correct SCM integration ID. The UI then cannot associate the repo with the intended GitHub environment, so actions and navigation break even though the repository name still appears in inventory.

Resolution

  1. In Aqua Supply Chain Security, open Repositories (or equivalent SCM view).
  2. Identify the affected repository (for example, org-name/repository-name).
  3. Remove the orphaned entry if it is duplicate or non-functional.
  4. Re-add the repository through the correct GitHub integration (the named environment, not the generic GitHub placeholder).
  5. Trigger a manual scan to force metadata to re-anchor to the correct integration ID.
  6. Confirm the repository is clickable, scans run, and findings (vulnerabilities, misconfigurations, SAST, etc.) display as expected.

Monitor after recovery

  • Watch the repository for 24–48 hours to ensure automated sync does not revert the mapping.
  • If duplicates or generic GitHub entries reappear, collect repository name, integration names, and timestamps and contact Aqua Support for backend investigation.

Verification and Monitoring

CheckExpected after fix
Repository link in UIOpens repository details
Integration columnShows named GitHub environment, not orphaned generic entry
Manual scanCompletes; results visible on dashboard
Integration ID alignmentSame integration ID as sibling repos in the same GitHub environment

Important Considerations

  • Use the same GitHub App or PAT integration consistently when re-adding repositories.
  • Avoid parallel duplicate registrations of the same repo under different integrations.
  • Document which GitHub organization/environment owns each repo to speed re-linking.

Platform Coverage

  • Component: Supply Chain Security — GitHub SCM integration
  • Platforms: Aqua SaaS