Several other Linux Twitter clients have also fallen in the APIcalypse, such as Polly and Turpial, which is a shame as they were both great clients. They apparently had plenty of time to prepare for the API 1.0 shutdown so what gives? This means I probably may not spent quite so much time on Twitter, though I do still have a good usable Twitter client on my Android devices, which is Plume. If anybody knows of a usable Linux native Twitter client that works now, please suggest one in the comments!
Update 13/06/13: I have discovered a fairly new native Twitter client called Birdie, it's a little lacking in configuration options at the moment but it mostly does what I need it to. One thing I'd like is a "reply all" option. Also being in development, it is a little crashy!
I have found out to get Polly working again you need to install the latest builds from the Daily PPA. And it's stable, though I do find the default layout a little simplistic, I went into File and New Stream and added a Mentions stream. Also Search is not yet implemented either. For me, it's not as nice as Hotot was but it will have to do for now.