Century 24 Solutions (C24) is a London-based company whose software I have been using for a few years now. Integration Objects (IO) is a very complete Java-based program for data modelling and transformation. I started using it because I needed to produce hundreds of Schemas with shared definitions for a client, and Schema "includes" would have been too hard to manage. I wanted a repository-style tool that would just let me select which types are required in which Schemas, and then generate the Schemas without includes. [As a bonus, IO also generated Java representations of the Schemas and binding code to read/write XML to/from Java.]
The truth is, there are very few repository-style tools out there that can do this, and the only one that was sufficiently close to getting it right, in my opinion, was C24 IO. The fact that I had a lot of input into the addition of XML Schema support to the tool may have something to do with that. They produced the tool that I needed to do the job.
C24 IO has been able to do XPath on Java objects for years now, but what is new is that recently they brought in Mike Kay (a fellow member of the XML Guild) to implement XQuery for Java objects. I'm pretty sure C24 are right when they say that this is the first ever implementation of XQuery for Java objects. It will certainly be a very useful addition to the tool. XPaths are very useful, but there is still a limit to what they can do. XQuery can do so much more, and the syntax is pretty familiar for anyone who has a basic working knowledge of SQL and XML.
This isn't just a solution looking for a problem, by the way. I know the guys at C24 well enough that I know they added XQuery support because one of their biggest customers wanted the ability to do XQueries on in-memory Java objects (after all, it makes no sense to have to serialise all of your Java objects to XML just to be able to run a query).
C24 IO is very cool piece of software, it's worth your time to download a copy of the Open Edition to have a play with. There's a bit of a learning curve at the start, because you've probably never used a tool quite like it. However, there's a lot you can get out of it - like XQuery.