Found one Java-level deadlock:
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"Handling GET /jenkins/view/Portal/ : RequestHandlerThread[#12]":
  waiting to lock monitor 0x000000001a449d08 (object 0x0000000419d757e8, a hudson.ExtensionList$Lock),
  which is held by "QueueSorter.installDefaultQueueSorter"
"QueueSorter.installDefaultQueueSorter":
  waiting to lock monitor 0x000000001ae56c48 (object 0x000000041895e0f0, a hudson.model.Queue),
  which is held by "Queue.init"
"Queue.init":
  waiting to lock monitor 0x000000001a449d08 (object 0x0000000419d757e8, a hudson.ExtensionList$Lock),
  which is held by "QueueSorter.installDefaultQueueSorter"