I'm not sure whether it's better from a performance perspective (initial data transfer size vs. caching vs. percent of all css/js that is used on any given page) to bundle every single JS plugin and CSS file into one CSS file and one JS file that get included on every page, but from a maintainability perspective I feel like it definitely hurts.

Before, you have a CSS file at the top of the same template where the HTML that uses those styles lives (and only that template), so if you're trying to figure out where some style comes from it's pretty obvious.  Now you're dealing with a minified CSS file with the entire site's styles in it and bleh...

I'm in favor of keeping hqstyle (which I really believe should be part of hqwebapp anyway, with hqbootstrap being the only submodule) limited to bootstrap and a core set of modifications to it, while putting everything else in individual files in hqwebapp/static or the appropriate app that goes with a given CSS or JS file.