The main problem is that for doing that I need to make a mod, I don't wan't to make any mods for that, simply because if any other mod change my modded class, it will serve nothing ... and because i need to update the mod for all versions, including snapshot versions, custom server launcher and very very old version.
Before I installed FML, all mods worked fine, found the mods and files in the good place.
The problem must be in FML, or I have forget one option ...
( Before I make this version, my program clean and copy the minecraft versions in the .minecraft, waiting between 2 and 5 minutes for starting minecraft is not a very good solution ..., and I have more that 20 versions of minecraft, )
EDIT : If it determine the folder with Minecraft.getMCDir, why it don't looks in my "/home/user/.mcm/version/test/.minecraft" or "/home/user/.minecraft" instead of "/home/user/.mcm" ?