Merge branch 'develop' into Release_2_9_0b1_Branch

diff --cc help/html/features/groovy.html
Simple merge

diff --cc help/html/releases.html
Simple merge

diff --cc help/html/whatsNew.html
Simple merge

diff --cc src/jalview/analysis/AlignmentUtils.java
Simple merge

diff --cc src/jalview/appletgui/AlignFrame.java
Simple merge

diff --cc src/jalview/bin/Jalview.java
Simple merge

diff --cc src/jalview/bin/JalviewLite.java
Simple merge

diff --cc src/jalview/datamodel/AlignmentAnnotation.java
Simple merge

diff --cc src/jalview/datamodel/Mapping.java
Simple merge

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/Desktop.java
Simple merge

diff --cc src/jalview/io/BioJsHTMLOutput.java
Simple merge

diff --cc src/jalview/io/FeaturesFile.java
Simple merge

diff --cc src/jalview/io/JSONFile.java
Simple merge

diff --cc src/jalview/javascript/MouseOverStructureListener.java
Simple merge

diff --cc src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
Simple merge

diff --cc src/jalview/json/binding/biojson/v1/AnnotationPojo.java
Simple merge

diff --cc src/jalview/schemes/UserColourScheme.java
Simple merge

diff --cc src/jalview/ws/DBRefFetcher.java
Simple merge

diff --cc src/jalview/ws/uimodel/AlignAnalysisUIText.java
Simple merge

diff --cc test/jalview/analysis/ParsePropertiesTest.java
Simple merge

diff --cc test/jalview/io/JSONFileTest.java
Simple merge

diff --cc test/jalview/util/MappingUtilsTest.java
Simple merge