Hi Jason,
https://github.com/BaseXdb/basex-examples/blob/master/src/main/java/org/base...
in order to make the example work, you first need to run XMLDBCreate. I have extended the JavaDoc to point to this issue.
Also, any update on the status of March 2011 regarding the questions: Is it possible to create child Collections within a database through the XMLDB API?
In BaseX, databases and collections are similar concepts. See e.g. [1] for more information on how we handle databases, collections and documents.
Best, Christian