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> As such I suspect the build tooling never looks at the app_usecases.xml file because it's not explicitly included anywhere while the validation checks run on all XML files in the repository. 

Yes, that's correct, it validates the wrapper "book" file and anything
that's included in it, but not other files that might be in the source
directory. Btw., the clouddocs-maven-plugin does now check IDREFs for
corresponding IDs. Older versions were not checking that due to a bug.

David