I have everything stored in GameData even if the Addon was not made for the new structure but everything works fine! Mechjeb is loaded and all the other Addons i normally use. I just can't load any ship stored in the GameData directory but only if they're stored in either Ships directory or below Saves. To be honest there is still a big problem with the new system. You have a savegame with some flights active. One of the ships uses a part contained in a mod. The mod gets updated and moves its files from KSP_OS\Parts to GameData. Now the internal USL to the parts is different. If you load your savegame you get an error that a ship could not get loaded because of missing parts. your flights are cancelled and the game automatically saves your game. You sucessfully destroyed your whole savegame! If you now put the missing parts back into the KSP_OS\Parts directory and try to load that savegame again: fail. the game already overwrote it just as the error message appeared the first time. I really don't know why we have to invent the wheel again. Back at Quake 1 times such a system already existed. stock files are stored in these pak files (ordinary zip files) and all custom (modded) files are stored in the same directory but with subdirectories, etc. That system didn't had the problem with different internal urls ...