After a fair bit of web searching and hacking, the following information should enable you in the configuration of your Logitech Harmony Remote and installation of client interfacing software on Linux to update your universal remote.
These instructions were compiled using Linux Mint 17 (Qiana) x86_64 and Firefox 34 at the time of writing.
The following is a list of identified libraries and tools the subsequent software for using your Logitech Harmony Remote.
I started using FreeNAS in August 2013. It is fantastic piece of software and I have been really impressed by the upgrades just in the few months I've been using it. It looks like they recently went to a plugin system as of version 9 to make installing software easier for end users. I've ran into several issues related to plugins and user + group permissions so I decided to just use the available FreeBSD port system. After fiddling for a few days (now turned into months) I believe I have created something helpful for the community and anyone interested in picking up the port system. The sandbox nature of FreeNAS's jail system is especially helpful for playing around without having any consequence on your core system.
Here are straight-forward instructions to setting up a bunch of different software on FreeNAS. If you make a terrible error, just throw up another plugin sandbox and repeat.