Merge branch 'develop' into Release_2_9_0b1_Branch

JAL-1894 update next-release branch for build system

diff --cc build.xml
Simple merge

diff --cc doc/UnitTesting.html
Simple merge

diff --cc examples/applets.html
Simple merge

diff --cc examples/javascript/jalview.js
Simple merge

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

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

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

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

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

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

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

diff --cc src/jalview/commands/EditCommand.java
Simple merge

diff --cc src/jalview/datamodel/AlignedCodonFrame.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/AlignViewport.java
Simple merge

diff --cc src/jalview/gui/Jalview2XML.java
Simple merge

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

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

diff --cc src/jalview/io/FormatAdapter.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/jbgui/GAlignFrame.java
Simple merge

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

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

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

diff --cc test/jalview/commands/EditCommandTest.java
Simple merge

diff --cc test/jalview/datamodel/AlignedCodonFrameTest.java
Simple merge

diff --cc test/jalview/datamodel/AlignedCodonIteratorTest.java
Simple merge

diff --cc test/jalview/datamodel/AlignmentTest.java
Simple merge

diff --cc test/jalview/io/Jalview2xmlTests.java
Simple merge

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