I've already done that. I can launch MD.EMU directly from the launcher, it's the same job as you've done, edit the decompiled classes.dex. I can run Genesis and SMS games when they are compressed as .7z. Unfortunately I couldn't launch a SegaCD game from the launcher, but I could load it using "am start". I don't think it worth sharing this modified launcher as my Genesis Flashback HD is the .obb version and messing with the launcher can 'brick' the console.
Now I'm trying to build MD.EMU with the key mapping from the Genesis Flashback HD. I already found the files and remapped them, but build it tricky as the source is near impossible to be compiled. I could compile the "imagine" and "EmuFramework" but it's failing to compile the emulator itself. I will try to do that on the weekend but I'm not sure if it will work. If I have any progress I will share with you all.