Well, code coverage works now, and looks like a great first cut. Some quick notes, before I put all this in JIRA.
1) It looks like covered classes and paths are not being persisted with the run profile, although coverage toggling is. Check your serialization code.
2) It is probably adequate to toggle coverage viewing on a per-project basis. The current per-file basis toggling is far too clunky. A toggleable toolbar button would be sweet.
3) In this fallen world, it actually is important to have some coverage count reports, rather than just editor highlighting. A toolwindow with per-class percentages and rollups would be fine, although annotating the project window might be even nicer.
4) I've never had a use for the "how many times was this line executed" information that some tools give, but if it's easy to do, it might be worthwhile. Maybe in the editor gutter, like VCS annotations or line numbers.
5) The auto-merge and auto-synchronization with editing changes ROCK MIGHTILY!!!!! All on it's own, that technology is enough to differentiate your coverage tool from all competitors. That said, you do need to blow away the accumulated coverage information for a project. It's not so much that it is necessary to fix things if you get out of sync, but to allow coverage to be measured for different test suites.
6)It is more important to see uncovered code than covered code, so there should be gutter coloring for both.
7)You might wish to allow background coloring, rather than just gutter coloring.
8)Colors need to be configurable, but you knew that already.