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@schlessera I enabled 'Automatically delete merged branches' on all of the repositories and removed the Delete Merged Branch app.
Also, I removed the Settings app because it comes with this issue:
WARNING: Note that this app inherently escalates anyone with push permissions to the admin role, since they can push config settings to the master branch, which will be synced. In a future, we may add restrictions to allow changes to the config file to be merged only by specific people/teams, or those with admin access (via a combination of protected branches, required statuses, and branch restrictions). Until then, use caution when merging PRs and adding collaborators.
Until restrictions are added in this app, one way to preserve admin/push permissions is to utilize the GitHub CodeOwners feature to set one or more administrative users as the code owner of the .github/settings.yml file, and turn on "require code owner review" for the master branch. This does have the side effect of requiring code owner review for the entire branch, but helps preserve permission levels.
GitHub will delete merged branches for us, so we don't need Delete Merged Branch app anymore.
Done is:
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