Hi Will,

.query.xml files will be used for metadata for both "real" database tables and for custom LabKey SQL queries. It's legit, for example, to have an AssayLookup.query.xml file without a corresponding .sql file to go with it. It should go in a subdirectory that matches the schema name, as exposed through the query schema browser. Usually that matches with the underlying database schema name, but not always. This is the module-based equivalent to applying the XML though the schema browser.

For a map of where to put the file, look here:

https://www.labkey.org/wiki/home/Documentation/page.view?name=moduleDirectoryStructures

Thanks,
Josh