The correct tool is the 'Import Wizard' in CE 8.5. Don't bother trying to use it, if you haven't applied the latest patches - early versions had bugs. It will import folders (friendly name and all) and instances (look for the check box on the target APS specification dialog). Lots of instances at once will take a loonng time and may choke leaving your system db in a questionable state. When migrating folder and subfolders it's best to pick a folder at the root of the aps and get all subfolders (and instances) on one import, because the next pass will duplicate the higher level folders with '(2)' subscript. Nice! If report ownership is important to you, import the users ahead of time. If the report owner is not there when the report is imported, the owner will become ADMINISTRATOR.
No help on the source control.