Any file that gets written from an AppGameKit app goes to the sandbox aria for the app (and you can't change that in Tier 1).
On Windows, it is the documens\agk\<apname> directory (and a subdirectory under that if specified).
On Android and iOS it is to other places.
If you have a file in your media directory that you 'overwrite', it ends up in the sandbox area.
If you go to open a file, AppGameKit first looks in the sandbox area and then the app area (<app>/media for Tier 1 and <app> for Tier 2).
If you delete a file from AppGameKit, it will only delete the one in the sand box area.
Apps may not add or make changes to the default app directory.
Cheers,
Ancient Lady
AGK Community Tester and AppGameKit Master