Late on Tuesday evening, I successfully got a branch of Choob to run without its 'Object DB'. Presently, it runs only a few of the more simple plugins - for instance, the 'Alias' plugin is not supported, so I spent a couple of minutes trying to work out why it wasn't replying to commands.
With ODB gone, vast swathes of complicated parsing code can be removed from the bot's core. JJTree should no longer be needed to compile the bot. The next step is probably to consolidate the core database code using Hibernate, and then get the more complicated plugins to work again.
Orthogonally to this, I'd like to kill HorriblePerlScript.java, and perhaps also design a nicer plugin system that lets Eclipse work with plugins as (shock) actual Java files. I suspect I'd need some help with that, though.