Hi Will,

resources/schemas/SCHEMANAME.xml points at tables in the "real" underlying database.

resources/queries/SCHEMANAME/TABLENAME.query.xml points at tables in the schema/queries that are exposed through the schema browser.

They often line up identically, but in the case of the assay runs tables, the real database table is exp.experimentrun, while the assay schema exposes a filtered view for a specific assay design under the assay.ASSAY_TYPE.ASSAY_DESIGN schema.

Thanks,
Josh