I’ve update the Unity Soft Debugger add-in so that it is compatible with MonoDevelop 5 (or Xamarin Studio 2). It is available in the Beta channel of the add-in manager.
As this is a direct update from the previous version of MonoDevelop the plugin should still work for Unity 3.5 users. Similarly some the start/stop bug may also exist. Soon I’ll merge in any updates/bug fixes from the Unity repository.
More information about this add-in can be found on the original blog post: MonoDevelop 4 (Xamarin Studio) Debugging for Unity
After speaking to on of the kind developers at Unity3D who works on the MonoDevelop port it turns out that they have released some of their plugins for the latest version of Xamarin Studio through their website, as a beta, so that developers can use them.
For this reason I will no longer be maintaining this project. The sources in Github will remain available for users of Unity 3.5 and Unity 4.