Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

resolved conflicts and adapted to some upstream changes. no detailed functional testing as yet (see next commit :) )

 Conflicts:
	resources/lang/Messages.properties
	resources/lang/Messages_es.properties
	src/jalview/api/AlignViewportI.java
	src/jalview/bin/Jalview.java
	src/jalview/datamodel/Sequence.java
	src/jalview/datamodel/SequenceI.java
	src/jalview/gui/AlignFrame.java
	src/jalview/gui/JvSwingUtils.java
	src/jalview/gui/OverviewPanel.java
	src/jalview/gui/PopupMenu.java
	src/jalview/gui/SplitFrame.java
	src/jalview/gui/WsJobParameters.java
	src/jalview/io/AlignmentFileReaderI.java
	src/jalview/io/FileLoader.java
	src/jalview/io/StockholmFile.java
	src/jalview/jbgui/GAlignFrame.java
	src/jalview/jbgui/GPreferences.java
	src/jalview/renderer/AnnotationRenderer.java
	src/jalview/viewmodel/AlignmentViewport.java
	src/jalview/ws/jws2/Jws2Discoverer.java
	test/jalview/analysis/AAFrequencyTest.java
	test/jalview/gui/AlignFrameTest.java
	test/jalview/gui/AlignViewportTest.java