I'm not crazy about splitting the books up further than they already are. If all you want is the Mecha stuff from Mecha & Manga, you can just ignore the other feats / powers / and so on; I'd rather keep it simple for the newbies, so they can turn mecha & manga on and off with a single click, than requiring multiple clicks for each book. "What do you mean, I have to click 5 times to turn on all the Mecha & Manga stuff?"
BTW, thanks for the files, Duggan - I'll take a look at these and try and figure out the problem.

Well, you can always set it up with an upper-level checkbox that turns them all on or all off, but whatever works for you. I still wish I'd figured out a better way to handle Pet/Menagerie/etc. As it is now, there's no real purpose in having those feats since you can do the exact same thing with Minion, more easily so in some cases.
And no problem on the sending files. I'm kind of with the "by default off" myself, simply because there are enough exceptions, and the check is really something you'd be doing on a finished hero. If I might make a suggestion, you already have the attack and damage bonuses on Special tab. If you parse those (and add in ranks of Sneak Attack and Favored Opponent), you've got a simple way of checking that at least one attack meets caps (Don't forget to discount the accidental attack bonus on non-targetted areas). Oh, and I found that your current check doesn't discount temporary conditions. Being flat-footed made one of my characters flag as being under caps on defense/toughness.
Some things that haven't been fixed yet:
* Aura adding to Unarmed damage on the Special tab
* Sneak Attack and Favored Opponent counting toward caps (or at least I don't think this is applying at the moment)
* Area progression feats don't change the text on the Areas (as noted in a prior post, Nullifying Field does do this, so it seems a bit odd that the other Areas extras don't)
* I need to do more tests on this at home, but the Reset button on In-Play listed "2 conditions" for one of my characters, I think because he had Bruised and Injured. Clicking the Reset button did not reset those.