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Currently, the application discovery feature does not consider nor display that the discovered app is deployed via Publisher. If it is, then arguably, it should be viewed as a managed app. At the very least, the presence of a Publisher deployment ...
Publish only newly selected apps from catalog on sync
When adding in new apps from the catalog, allow the ability to publish only newly selected apps to prevent all applications from getting an update that will be deployed when not wanted.
Different companies do source folders differently it would be nice to change/affect the structure that is created. For example creating an app that has the same name as the source folder would make it easy to track the what source folder is attach...