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they (dml, ddl, xmldb...) never have been a valid subsystem component. Hence, all those @pakage tags are incorrect but we have been keeping and using them. So, the checker is formally correct.
Recently we added both dml and ddl as valid core APIs (link). And I imagine that at some point, with the move to autoloaded classes... all them will end there, within the lib/classes/[dml|ddl] directories and within namespace \core\dml\moodle_database and friends.
Then, all those packages / categories will be fixed once and forever. In the mean time they will keep being (formally) incorrect.
The CiBot reports a false negative error of "Package core_dml is not valid" when running the PHPDocs style problems section.
See https://integration.moodle.org/job/Precheck%20remote%20branch/95931/artifact/work/smurf.html#phpdoc
However core_dml appears to be used throughout the lib/dml folder. See https://github.com/moodle/moodle/blob/master/lib/dml/moodle_database.php#L20
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