Mod Manager It's about 3 years old now, and supports a lot of things: Contrary to the title of my program it supports far more than Coalesced mods (v1 only supported coalesced, as we didn't have DLC editing back then).
If you haven't seen ModMaker, you should really try it out, it saves tons of time, and you can fork other peoples mods. It works with my online Coalesced editor, ME3Tweaks ModMaker. I've got a couple thousand active users based on some telemetry on my site. I have just released Version 4 Beta 1 of my Mod Manager tool that acts as a mod installer/uninstaller for files in Mass Effect 3.