GitHub App Automated permissions configuration

I want to automate the process of updating the permissions for GitHub apps.  The “repo-content” doesn’t seem to allow us to update the permission.  It looks like the api only supports configuring content per repo and not for all repositories under an organization.  

I’m not certain what you mean by “automate updating the permissions for GitHub apps”. Are you trying to build an app that accepts updated permissions for GitHub Apps in an organization? This shouldn’t be possible because it would defeat the purpose of requiring asking permission of the organization administrators in the first place.

If I’m not understanding, can you give some more information on what it is you’re trying to do?