JAL-3446: Merge Jalview-JS/JAL-3253-applet branch to Jalview-JS/develop

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CR-JAL-231 0

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    Objectives

    Merge the 'JS applet' branches changes, identifying any conflicts or other changes that need closer inspection.

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    /doc/JalviewJS-API.md Changed
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    /doc/JalviewJS-startupParams.md Added
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    /doc/JalviewJS-startupParams.xlsx Added
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    /j11lib/Jmol-14.29.17-no_netscape.jar Deleted
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    /j11lib/Jmol-14.29.17-no_netscape.jar Deleted
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    /j11lib/Jmol-15.1.3.jar Added
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    /j11lib/Jmol-15.1.3.jar Added
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    /j8lib/Jmol-14.29.17.jar Deleted
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    /j8lib/Jmol-15.1.3.jar Added
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    /src/jalview/.../scoremodels/ScoreModels.java Changed
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    /src/jalview/analysis/AlignmentSorter.java Changed
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    /src/jalview/analysis/CrossRef.java Changed
    /src/jalview/api/JalviewJSApi.java
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    /src/jalview/api/JalviewJSApp.java Deleted
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    /src/jalview/appletgui/APopupMenu.java Changed
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    /src/jalview/appletgui/AlignFrame.java Changed
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    /src/jalview/appletgui/AlignViewport.java Changed
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    /src/.../appletgui/RedundancyPanel.java Changed
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    /src/jalview/appletgui/SeqPanel.java Changed
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    /src/jalview/appletgui/TreeCanvas.java Changed
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    /src/jalview/bin/AppletParams.java Changed
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    /src/.../bin/ApplicationSingletonProvider.java Added
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    /src/jalview/bin/ArgsParser.java Changed
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    /src/jalview/bin/Cache.java Changed
    /src/jalview/bin/Jalview.java Changed
    /src/jalview/bin/JalviewJS2.java Changed
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    /src/jalview/bin/JalviewJSApi.java Deleted
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    /src/jalview/bin/JalviewJSApp.java Changed
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    /src/.../features/FeatureAttributes.java Changed
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    /src/jalview/.../features/FeatureSources.java Changed
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    /src/.../features/SequenceFeatures.java Changed
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    /src/jalview/datamodel/Alignment.java Changed
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    /src/jalview/datamodel/PDBEntry.java Changed
    /src/jalview/ext/ensembl/EnsemblCds.java Changed
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    /src/jalview/ext/ensembl/EnsemblGene.java Changed
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    /src/jalview/.../ensembl/EnsemblSeqProxy.java Changed
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    /src/jalview/fts/core/GFTSPanel.java Changed
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    /src/jalview/.../service/pdb/PDBFTSPanel.java Changed
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    /src/jalview/.../pdb/PDBFTSRestClient.java Changed
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    /src/.../uniprot/UniProtFTSRestClient.java Changed
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    /src/jalview/.../uniprot/UniprotFTSPanel.java Changed
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    /src/jalview/gui/AlignExportOptions.java Changed
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    /src/jalview/gui/AlignFrame.java Changed
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    /src/jalview/gui/AlignFrame.java Changed
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    /src/jalview/gui/AlignViewport.java Changed
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    /src/jalview/gui/AlignmentPanel.java Changed
    /src/jalview/gui/AnnotationChooser.java Changed
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    /src/.../gui/AnnotationColourChooser.java Changed
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    /src/jalview/gui/AnnotationExporter.java Changed
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    /src/jalview/gui/AnnotationLabels.java Changed
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    /src/jalview/gui/AnnotationPanel.java Changed