Can an enterprise-installed GitHub App access every repository in the enterprise?
No. Enterprise installations manage enterprise-level resources and do not automatically receive organization or repository permissions. To work with organization or repository resources, an app must also be installed on each relevant organization or repository.
Answered in
GitHub App Enterprise Installs Expand Automation—With Important Permission BoundariesGitHub’s enterprise-installation GA expands app permissions for admin workflows, but repository access and webhooks still require separate installations.
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