I feel my explanations are generally clear, especially in light of the context I offered, and I don't want to keep repeating myself.
Sorry, Eric. I assume no one here wanted to steal your valuable time. But if you are seeking help, it’s sometimes helpful to help others first.
The plan had been to prototype using a Bash script and query files, […]
That piece of information was helpful, for example. If you use the Bash, you will treat BaseX as a standalone application. You’ll definitely have more freedom if you use Java: For example, you can prevent BaseX from reading the configuration from disk [1]. See [2] for some more code examples.
Have fun! Christian
[1] https://github.com/BaseXdb/basex/blob/da1e55d0214e44c1532f121c282021db50a9aa... [2] https://docs.basex.org/wiki/Java_Examples