I've read Topic:Uqs4b6a7u20b4fsu. I'm running MW 1.31.1, PHP 7.2, Apache2 with APCu.
If I import a large number of XML-exported pages via Special:Import, the categories for those pages aren't populated until I edit and save a new revision on each page, or run a bot to touch each page without revising them.
Topic:Uqs4b6a7u20b4fsu strongly suggests this is a symptom of the job queue not having been run, but I've got the runJobs.php maintenance task running every 30 seconds. The topic also suggests running refreshLinks.php to force reparsing the page; this also does not work.
Are there any other options that don't require running a bot across all of the imported pages after each import?