concurrent modification exceptions during CLI tests

Occasional test failure observed:

Caused by: java.util.ConcurrentModificationException
at java.base/java.util.HashMap$HashIterator.nextNode(HashMap.java:1511)
at java.base/java.util.HashMap$KeyIterator.next(HashMap.java:1534)
at jalview.workers.AlignCalcManager.getRegisteredWorkersOfClass(AlignCalcManager.java:310)
at jalview.viewmodel.AlignmentViewport.updateConsensus(AlignmentViewport.java:859)
at jalview.viewmodel.AlignmentViewport.alignmentChanged(AlignmentViewport.java:1873)
at jalview.gui.AlignmentPanel.alignmentChanged(AlignmentPanel.java:213)
at jalview.gui.AlignFrame.setAnnotationsVisibility(AlignFrame.java:5845)
at jalview.bin.Commands.processLinked(Commands.java:374)
at jalview.bin.Commands.processArgs(Commands.java:109)
at jalview.bin.Jalview.doMain(Jalview.java:841)
at jalview.bin.CommandsTest.callJalviewMain(CommandsTest.java:78)

There are lots of calls to setAnotationsVisibility - this method was never hardened to be thread safe - but could do some minimal patching.