merge-update from trunk

diff --combined .gitattributes
index fb3688ef79bc9d66665c09988cefeba1a85249f4,0a98a61bf49434baaffae5513022449514b69890..0de962a860089f2afb404cd1115360ae0ef95aad
--- 1/.gitattributes
--- 2/.gitattributes
+++ b/.gitattributes
@@@ -366,11 -366,6 +366,11 @@@ eu.etaxonomy.taxeditor.editor/icons/emb
  eu.etaxonomy.taxeditor.editor/icons/leaf_detail.png -text
  eu.etaxonomy.taxeditor.editor/icons/link_obj.gif -text
  eu.etaxonomy.taxeditor.editor/icons/xper64.png -text
 +eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/commons-lang3-3.1.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar -text
  eu.etaxonomy.taxeditor.editor/p2.inf -text
  eu.etaxonomy.taxeditor.editor/plugin.xml -text
  eu.etaxonomy.taxeditor.editor/pom.xml -text
@@@ -396,21 -391,14 +396,21 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditorInput.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/handler/EditCdmAuthoritiesHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditNewTaxonHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditSequenceHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/FixClassificationHierarchyHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenAlignmentEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenChecklistEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenDerivateViewHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenParentHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenTaxonEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SaveAllHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SaveTaxonHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ShowPherogramHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SpecimenPropertyTester.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/TaxonParameterConverter.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ToggleInsertOverwriteHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ToggleLeftRightInsertionHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewNameHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewPersonHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewReferenceHandler.java -text
@@@ -438,12 -426,6 +438,12 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/CreateNodeOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/DeleteNodeOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/RefreshNodeNumberingOperation.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CDMAlignmentObjectPlaceholder.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text
@@@ -632,10 -614,7 +632,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidationProblemsView.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorClassMarkerField.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorMessageMarkerField.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1 -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1 -text
  eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text
  eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text
  eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/Application.java -text
  eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/ApplicationActionBarAdvisor.java -text
@@@ -669,7 -648,6 +669,6 @@@ eu.etaxonomy.taxeditor.feature/LICENSE.
  eu.etaxonomy.taxeditor.feature/README.txt -text
  eu.etaxonomy.taxeditor.feature/build.properties -text
  eu.etaxonomy.taxeditor.feature/build.properties.with.jre -text
- eu.etaxonomy.taxeditor.feature/build.properties.wo.jre -text
  eu.etaxonomy.taxeditor.feature/feature.xml -text
  eu.etaxonomy.taxeditor.feature/pom.xml -text
  eu.etaxonomy.taxeditor.help/.classpath -text
@@@ -1870,7 -1848,6 +1869,6 @@@ eu.etaxonomy.taxeditor/README.txt -tex
  eu.etaxonomy.taxeditor/deploy_nightly.sh -text
  eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product -text
  eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product.with.jre -text
- eu.etaxonomy.taxeditor/eu.etaxonomy.taxeditor.product.wo.jre -text
  eu.etaxonomy.taxeditor/plugin_customization.ini -text
  eu.etaxonomy.taxeditor/pom.xml -text
  eu.etaxonomy.taxeditor/rcp.target -text

diff --combined eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
index 1918eca032d18ca826791d9bb4d1adad4eff554c,757c5cea551138aa93df010eae2463e8ddd0e854..54ae0db6fcb650ca4e313e0ffb8ac368a7db82b6
--- 1/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
--- 2/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
@@@ -2,7 -2,7 +2,7 @@@ Manifest-Version: 1.
  Bundle-ManifestVersion: 2
  Bundle-Name: Editor Bundle
  Bundle-SymbolicName: eu.etaxonomy.taxeditor.editor;singleton:=true
- Bundle-Version: 3.5.0.qualifier
+ Bundle-Version: 3.5.1.qualifier
  Bundle-Activator: eu.etaxonomy.taxeditor.editor.internal.TaxeditorEditorPlugin
  Bundle-Vendor: %Bundle-Vendor.0
  Bundle-Localization: OSGI-INF/l10n/plugin
@@@ -177,11 -177,4 +177,11 @@@ Bundle-ClassPath: .
   jdimodel.jar,
   pdebuild.jar,
   compatibility.jar,
 - junit.jar
 + junit.jar,
 + lib/biojava3-alignment-3.0.7.jar,
 + lib/biojava3-core-3.0.7.jar,
 + lib/core-1.8.5.jar,
 + lib/sequencing-1.8.5.jar,
 + lib/bioinfweb.commons/,
 + lib/LibrAlign/,
 + lib/commons-lang3-3.1.jar