Congruity is a Linux based gui for the Logitech Harmony website at http://members.harmonyremote.com/EasyZapper/UserHome.asp. The site should be familiar if you've ever run Logitech's own software under Windows.
Now, Congruity is a bit confusing if you're just starting it up and plugging it in, because on its own, it doesn't do anything. Congruity is based on command line software libraries called concordance/libconcord. Whatever the case, running apt-get install congruity under linux will install things for you.
So you want to update your harmony remote. What do you do now? You must go to the aforementioned harmonyremote.com web page first. You cannot simply run congruity. From there, you must follow the web based instructions after logging yourself in to your logitech user account.
Using Firefox, at various points you will be asked to either plug in your Harmony Remote, or download a file and run it with Congruity.. which you must do every time it asks. It actually worked pretty well for me.
It'd be nice if there was some other repository for harmony remote control code files. It's somewhat disturbing to think that should something happen to logitech (not that its likely, but you never know) that great repository of codes will be unaccessible. It'd be nice if harmony remote owners could back up their codes to some other, perhaps more open site, to build a new secondary backup database that libconcord/congruity could be compatible with.
But for the time being, install was fast, and once I realized all you have to do is go to harmonyremote.com after installing congruity, everything went better than expected.