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Jalview builds sucessfully and runs from eclipse

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Add support RNAML format

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Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop conflicts due to refactoring according to JAL-972, JAL-968, JAL-968 Conflicts: .classpath examples/appletParameters.html src/jalview/appletgui/AlignFrame.java src/jalview/appletgui/AlignViewport.java src/jalview/datamodel/SequenceGroup.java src/jalview/gui/AlignFrame.java src/jalview/gui/AlignViewport.java src/jalview/jbgui/GAlignFrame.java

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groovy nature not needed in project

added notes on third party library licencing and updated netbeans builder library deps

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JAL-913; Documentation of RNA Structure Conservation

Change-Id: I695f08d01e4feba87b5c5f15981896f7ee484dd4

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Start merging of Laurens Code

Change-Id: Ic7501daa6075363a8f725ba2c6784cedefa27207

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share eclipse settings

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