Me & JM have been closing some GitHub issues via commit lately on the CMS, but the proper hook isn't being triggered to update the issue at the tracker application. This commit should have closed this tracker item but didn't.
Last I looked, this seemed to be working OK now.
I spent some time looking at this at CoderFaire with @jfryman (GitHub guy in Nashville) and we figured out that only a commit event gets triggered in this scenario. Neither of us could really answer whether this is intended behavior or a bug, and he indicated he'd do some research on the matter.
If it ends up being this is intended behavior, we'll have to implement a hook monitoring the commit event and manually parse the commit message to pick up that an issue is closed and handle it within our app. Of course, all of this is a moot point if we'd just stop manually committing and use GitHub PR's only, right @dbhurley ?