FYI I installed this today and started doing some testing. So far so good. One thing i noticed, which hopefully will be changed, is the generation of the tools. yml. It doesn't get generated until you use a tool ingame that mcmmo doesn't recognize. For instance, i had no config file until i made an rp2 ruby pickaxe and used it. I defined and tested out basic items like shovels, axes, swords, hoes, sickles. They all got xp and I was able to use the rightclick abilities correctly.
Dual use items like the ic2 drill need to be defined as both a shovel and a pickaxe, but work fine.(FYI for the drill ID i used 30234, not 30234:1. The :1 is just there to make the item look damaged, in effect giving it a power meter. the underlying item is still 30234, even if you never see it like that)
The nanosaber is an odd case, since it has a different item id when you activate the right click mode. I defined both IDs as a sword and got xp in both modes. Only bummer here is that right click is the mcmmo special ability key, same as the key to switch between normal and charged nanosaber mode.
If anyone plans on using this, the best way to do it by far is connect to your world and use NEI to find the ID of the items you want to define.