It didn't take as long as expected which means it's probably wrong. For non-filtered queries it's three times faster and for certain FILTER queries (with equals) it's 47 times faster (from 284 to 6 seconds). At least it's now in the same order of magnitude as most tools and it's a a tiny bit faster than some (although adding more features will probably slow it down again).
* AttributeValuePair has been removed and replaced with maps (as discussed previously).
* Seeing as though maps were used so much hashCode and equals were optimized. As I've found before (I think), isAssignableFrom is slower than try/catch for equals (depending on your usage of course).
* Queries go through unsorted and uncopied rather than standard graph finds. I'd forgotten about how much effort had gone into allowing remove and automatic sorting on iterators.
* A very simple optimizer (it's really only simplifying the FILTER constraints at the moment) was added. Tree manipulation was painful - I resorted to mutating in place operations.
* Better designed. It's a bit hard to qualify this except what was there was truly awful - objects being created in constructors and passing itself in. The nice thing about IoC is it's quite easy to see when you're not using objects at the same architectural level.
Update: For download.