Program: 91718
Project: 91718
Buggy source:
protected void computeResult(){
  MavenProject targetPOM=getTargetPOM();
  IMavenProjectFacade facade=MavenPlugin.getDefault().getMavenProjectManager().getMavenProject(targetPOM.getGroupId(),targetPOM.getArtifactId(),targetPOM.getVersion());
  Model targetModel=null;
  if (targetPOM.equals(getProjectHierarchy().getFirst())) {
    targetModel=model;
  }
 else {
    targetModel=loadTargetModel(facade);
    if (targetModel == null) {
      return;
    }
  }
  LinkedList<Dependency> dependencies=getDependenciesList();
  CompoundCommand command=new CompoundCommand();
  for (  Dependency dep : dependencies) {
    Command unset=SetCommand.create(editingDomain,dep,PomPackage.eINSTANCE.getDependency_Version(),SetCommand.UNSET_VALUE);
    command.append(unset);
  }
  DependencyManagement management=targetModel.getDependencyManagement();
  if (management == null) {
    management=PomFactory.eINSTANCE.createDependencyManagement();
    Command createDepManagement=SetCommand.create(editingDomain,targetModel,PomPackage.eINSTANCE.getModel_DependencyManagement(),management);
    command.append(createDepManagement);
  }
 else {
    for (    Dependency depFromTarget : management.getDependencies()) {
      Iterator<Dependency> iter=dependencies.iterator();
      while (iter.hasNext()) {
        Dependency depFromSource=iter.next();
        if (depFromSource.getGroupId().equals(depFromTarget.getGroupId()) && depFromSource.getArtifactId().equals(depFromTarget.getArtifactId())) {
          iter.remove();
        }
      }
    }
  }
  for (  Dependency dep : dependencies) {
    Dependency clone=PomFactory.eINSTANCE.createDependency();
    Command addDepCommand=AddCommand.create(editingDomain,management,PomPackage.eINSTANCE.getDependencyManagement_Dependencies(),clone);
    command.append(addDepCommand);
    command.append(createCommand(clone,dep.getGroupId(),PomPackage.eINSTANCE.getDependency_GroupId(),"String_Node_Str"));
    command.append(createCommand(clone,dep.getArtifactId(),PomPackage.eINSTANCE.getDependency_ArtifactId(),"String_Node_Str"));
    command.append(createCommand(clone,dep.getVersion(),PomPackage.eINSTANCE.getDependency_Version(),"String_Node_Str"));
  }
  editingDomain.getCommandStack().execute(command);
}

Fixed version (ground truth):
protected void computeResult(){
  MavenProject targetPOM=getTargetPOM();
  IMavenProjectFacade facade=MavenPlugin.getDefault().getMavenProjectManager().getMavenProject(targetPOM.getGroupId(),targetPOM.getArtifactId(),targetPOM.getVersion());
  Model targetModel;
  EditingDomain targetEditingDomain;
  CompoundCommand command=new CompoundCommand();
  CompoundCommand targetCommand;
  if (targetPOM.equals(getProjectHierarchy().getFirst())) {
    targetModel=model;
    targetEditingDomain=editingDomain;
    targetCommand=command;
  }
 else {
    targetModel=loadTargetModel(facade);
    if (targetModel == null) {
      return;
    }
    targetEditingDomain=findExistingEditorDomain(facade);
    if (targetEditingDomain == null) {
      targetEditingDomain=createDummyEditingDomain();
    }
    targetCommand=new CompoundCommand();
  }
  LinkedList<Dependency> dependencies=getDependenciesList();
  for (  Dependency dep : dependencies) {
    Command unset=SetCommand.create(editingDomain,dep,PomPackage.eINSTANCE.getDependency_Version(),SetCommand.UNSET_VALUE);
    command.append(unset);
  }
  DependencyManagement management=targetModel.getDependencyManagement();
  if (management == null) {
    management=PomFactory.eINSTANCE.createDependencyManagement();
    Command createDepManagement=SetCommand.create(targetEditingDomain,targetModel,PomPackage.eINSTANCE.getModel_DependencyManagement(),management);
    targetCommand.append(createDepManagement);
  }
 else {
    for (    Dependency depFromTarget : management.getDependencies()) {
      Iterator<Dependency> iter=dependencies.iterator();
      while (iter.hasNext()) {
        Dependency depFromSource=iter.next();
        if (depFromSource.getGroupId().equals(depFromTarget.getGroupId()) && depFromSource.getArtifactId().equals(depFromTarget.getArtifactId())) {
          iter.remove();
        }
      }
    }
  }
  for (  Dependency dep : dependencies) {
    Dependency clone=PomFactory.eINSTANCE.createDependency();
    Command addDepCommand=AddCommand.create(targetEditingDomain,management,PomPackage.eINSTANCE.getDependencyManagement_Dependencies(),clone);
    targetCommand.append(addDepCommand);
    targetCommand.append(createCommand(targetEditingDomain,clone,dep.getGroupId(),PomPackage.eINSTANCE.getDependency_GroupId(),"String_Node_Str"));
    targetCommand.append(createCommand(targetEditingDomain,clone,dep.getArtifactId(),PomPackage.eINSTANCE.getDependency_ArtifactId(),"String_Node_Str"));
    targetCommand.append(createCommand(targetEditingDomain,clone,dep.getVersion(),PomPackage.eINSTANCE.getDependency_Version(),"String_Node_Str"));
  }
  editingDomain.getCommandStack().execute(command);
  if (command != targetCommand) {
    targetEditingDomain.getCommandStack().execute(targetCommand);
  }
}