I've done some google searching and followed these tutorials http://mobile.tutsplus.com/tutorials/game-engine/using-version-control-with-unity3d/ and another website I can't find that pretty much said you can ignore all the folders except the Assets folder. So downloading the latest version Unity 4.2 and downloading the tutorial project Stealth, the folder directory structure for the stealth project looks like this StealthTest StealthTest/Assets StealthTest/Library StealthTest/ProjectSettings StealthTest/Temp <- This one disappears if you shut down Unity I did some testing and keeping the Assets folder while deleting everything seems to work, but the Prefabs folder in the Assets no longer displays correctly when I start up Unity. The prefabs are still there, but no image of the env_stealth_static shows up in the preview or when I drag it to the scene. With more testing done, it seems that you can delete Project Settings folder fine as it will be regenerated correctly, but the Library folder is a bit more complicated. In the Library folder, deleting the ScriptAssembilies and metadata folders seems to be ok as Unity will regenerate them and the Prefabs stay in tact despite the fact the preview remains a blue box now in the file icons, but show up fine in the preview window. But if I delete all of the Library folder, you get problems with the prefab. The bottom line is what is safe to ignore and what is critical for the unity project to be recreated correctly with almost everything in tact? Or what did I do wrong if the Assets folder is really the only thing you need?