Your description of the protocol is basically right. All metadata is shared in a torrent called a "meta torrent", which you get via other users as a signed info

Your description of the protocol is basically right. All metadata is shared in a torrent called a "meta torrent", which you get via other users as a signed infohash. After querying for the torrent over the DHT network, you begin downloading the files. You are right that the update checking system is pretty crude right now. I definitely plan on eventually updating over I2P. I will probably wait until I have implemented generic file-sharing and just piggy-back on that functionality to distribute updates. I plan on adding a welcome message that explains how to use the interface. I already have that in the Android version, but for whatever reason I skipped over it this time. I think on Windows and OS X, you can just double-click a JAR file and it will launch it with Java. Hopefully most users won't have to drop to the command line to run it. Right now it's quite slow to get an update -- especially when you are getting their metadata for the first time, which can take 5 minutes or more sometimes. I plan on working really hard to speed this up over the next few months.