I use the PortableApps.com Application Template 2.2 to create the basic directory layout. Among other things I add for example one folder named "Test" with various files in the folder Data. Then I create the launcher and installer.
If a now install the portable app with the nstaller, I detect that the folder Data contains no folder "Test". Why is that so?
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Thats to make sure user data (which resides in WhateverPortable/Data) doesnt get overwritten on an upgrade. If you want to have something in /Data, put it inside /App/DefaultData.
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