Merge branch 'develop' into JAL-1483_29dev

Merge branch 'develop' into JAL-1483_29dev
updated JAL-1483 with commits from 15th Dec-7th Jan 2015

Conflicts:
	.classpath
	src/jalview/api/AlignmentViewPanel.java
	src/jalview/appletgui/SeqPanel.java
	src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
	src/jalview/gui/AlignFrame.java
	src/jalview/gui/AlignViewport.java
	src/jalview/gui/AnnotationExporter.java
	src/jalview/gui/FeatureRenderer.java
	src/jalview/gui/FeatureSettings.java
	src/jalview/gui/Jalview2XML.java
	src/jalview/gui/Jalview2XML_V1.java
	src/jalview/gui/PopupMenu.java
	src/jalview/gui/SeqPanel.java
	src/jalview/io/BioJsHTMLOutput.java
	src/jalview/io/HtmlSvgOutput.java