Logitech Harmony on Linux

Using libconcordance and congruity, you can access the logitech website directly, then hit the update file and let congruity process the 2 hex files (it will hand them to you in the right order) to update your remote.  Here is the congruity interface processing the second one:

And with that, I think I crossed off the last app that I still had to keep a windows virtual machine around for.