Preventing users from deleting organization repositories
You can prevent members from deleting or transferring repositories in organizations on your GitHub Enterprise Server appliance.
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In the upper-right corner of any page, click .
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In the left sidebar, click Business.
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Under your business account's name, click Settings.
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In the Business settings sidebar, click Member privileges.
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Under "Repository deletion and transfer", review the information about changing the setting. Optionally, to view the setting's current configuration for all organizations in the business before enforcing the setting, click View the current configuration on your organizations.
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Under "Repository deletion and transfer", use the drop-down menu and choose a policy.