Overview

After connecting a GitHub organization to Aqua Supply Chain Security, the repository count in Aqua may be lower than in GitHub, or specific repositories may not appear in search even though they exist in the organization. This article covers integration settings that filter repositories, sync steps to refresh the inventory, and remediation when the integration connection is stale.


Understanding GitHub Repository Inventory in Aqua

Aqua imports repositories according to integration options and the repositories selected during onboarding. Settings such as Skip Archived exclude archived GitHub repositories from sync. Auto-scan new controls whether newly discovered repositories are scanned automatically but does not by itself fix a missing inventory if sync or selection did not include those repos.


Repository names in the UI normally appear in organization/repository form. If naming or search behaves inconsistently for a single organization, verify sync status and integration health before assuming a code-level defect.


Symptoms

  • GitHub organization shows more repositories than Aqua (for example 101 in GitHub vs fewer in Aqua)
  • Search in Code Repositories returns no results for a repository that exists in GitHub
  • Pull Repositories does not increase the count or update Last updated
  • Issue isolated to one GitHub organization after other orgs onboarded successfully


Troubleshooting Steps

1. Review integration filters

In the GitHub integration settings, confirm:


SettingEffect
Skip ArchivedArchived repos in GitHub are not imported when enabled
Repository selectionOnly selected repos are linked; full org import requires explicit selection or bulk select


Count how many repositories are archived in GitHub if Skip Archived is enabled.

2. Run a manual repository pull

  • Open Integrations → your GitHub integration.
  • Click Pull Repositories.
  • Wait until sync completes.
  • Note whether the repository count or Last updated timestamp changes.
  • Search again using organization/repository format.

3. Temporarily adjust archived handling (if appropriate)

If missing repositories are archived in GitHub:

  • Note the current Skip Archived value.
  • Temporarily disable skip-archived behavior if policy allows.
  • Run Pull Repositories again.
  • Restore the original setting after validation.

4. Collect diagnostics when sync still fails

If repositories remain missing:

  • Capture Supportability logs while running Pull Repositories.
  • Record a browser HAR file while reproducing search in the Code Repositories UI (Developer Tools → Network → Preserve log → Save as HAR).

Share logs with Aqua Support for correlation with backend sync jobs.

5. Re-create the GitHub integration

When configuration is correct but inventory remains wrong:

  • Document current repository selection requirements.
  • Remove the failing GitHub organization integration.
  • Re-integrate the organization and re-select required repositories.
  • Confirm selected repositories scan successfully and appear in search.

A support-led session may be used to validate counts and selection during re-integration.


Important Considerations

  • Organization names that end with numeric characters may exhibit separate UI naming or search behavior; if only one org is affected, open a support case for engineering tracking while using re-integration as a workaround for inventory gaps.
  • Search is case- and path-sensitive; use the full org/repo string shown in GitHub.


Verification and Monitoring

  • Repository count aligns with expected non-archived (or intentionally included archived) repos
  • Target repository appears in search and can be included in scan policies
  • Last updated on the integration advances after each pull


Platform Coverage


ItemDetails
ComponentSupply Chain Security
PlatformAqua SaaS
IntegrationGitHub