Q: In BaseX, what is the difference between a database and a collection? The BaseX documentation uses the word "collection" in a way that makes its meaning unclear. Is a collection simply another word for a database, or is it a distinct construct? If the latter, what commands are used to manipulate collections?

A: About Collections and Databases
The XQuery documentation does not speak about databases, but collections - thus there is the name collection to conform to the specs. Yet the specification does not define what a collection is, this is implementation dependent. While other systems like Marklogic allow multiple collections in a database, BaseX regards one collection as a single database.
From the BaseX Documentation Wiki:

In BaseX, a database is a pretty light-weight concept and can be compared to a collection.
  It contains an arbitrary number of resources, addressed by their unique database path.

It is easy and a cheap operation to join over documents from multiple collections/databases, so split up as seams reasonable to you. Actually using multiple databases instead of one can have a positive effect on concurrency.
Managing Databases in BaseX
Databases are managed using BaseX Commands.
Most of interest will be


*

*CREATE DB [name] ([input]): Create a new database with a given name and input document or XML fragment

*OPEN [name]: Open a database as default collection

*DROP DB [name]: Deletes a database


Managing Databases Using XQuery
For some operations there are also BaseX-specific XQuery-functions in the Database Module, but using them is somewhat restricted by XQuery Update's Pending Update List.
Disclaimer: I'm somewhat involved within the BaseX team.
