Program: 96807
Project: 96807
Buggy source:
public void generateFileDifferences(List<Artifact> endArtifacts,String diffPrefix,String nextParagraphNumber,String outlineType,boolean recurseChildren) throws OseeArgumentException, OseeCoreException {
  renderer.setOption("String_Node_Str",endArtifacts);
  renderer.setOption("String_Node_Str",nextParagraphNumber);
  renderer.setOption("String_Node_Str",outlineType);
  renderer.setOption("String_Node_Str",true);
  renderer.setOption("String_Node_Str",true);
  renderer.setOption("String_Node_Str",true);
  renderer.setOption("String_Node_Str",renderer.getBooleanOption(WordTemplateProcessor.PUBLISH_AS_DIFF));
  renderer.setOption(WordTemplateProcessor.PUBLISH_AS_DIFF,false);
  renderer.setOption("String_Node_Str",recurseChildren);
  IOseeBranch endBranch=renderer.getBranchOption("String_Node_Str");
  renderer.setOption("String_Node_Str",endBranch);
  IOseeBranch compareBranch=renderer.getBranchOption("String_Node_Str");
  TransactionToken startTransaction;
  if (compareBranch == null) {
    startTransaction=BranchManager.getBaseTransaction(endBranch);
    compareBranch=endBranch;
  }
 else {
    startTransaction=TransactionManager.getHeadTransaction(compareBranch);
  }
  TransactionToken endTransaction=TransactionManager.getHeadTransaction(endBranch);
  TransactionDelta txDelta;
  boolean maintainOrder=renderer.getBooleanOption("String_Node_Str");
  if (startTransaction.getId() < endTransaction.getId() || maintainOrder) {
    if (compareBranch.equals(endBranch)) {
      txDelta=new TransactionDelta(startTransaction,endTransaction);
    }
 else {
      txDelta=new TransactionDelta(endTransaction,startTransaction);
    }
  }
 else {
    txDelta=new TransactionDelta(startTransaction,endTransaction);
  }
  boolean recurseOnLoad=renderer.getBooleanOption(WordTemplateProcessor.RECURSE_ON_LOAD);
  Collection<Artifact> toProcess=recurseChildren || recurseOnLoad ? getAllArtifacts(endArtifacts) : endArtifacts;
  List<Change> changes=new LinkedList<>();
  ChangeDataLoader changeLoader=new ChangeDataLoader(changes,txDelta);
  IProgressMonitor monitor=(IProgressMonitor)renderer.getOption("String_Node_Str");
  if (monitor == null) {
    monitor=new NullProgressMonitor();
  }
  changeLoader.determineChanges(monitor);
  try {
    monitor.setTaskName("String_Node_Str");
    diff(changes,toProcess,diffPrefix,txDelta);
  }
 catch (  Exception ex) {
    OseeLog.log(Activator.class,Level.SEVERE,ex);
  }
}

Fixed version (ground truth):
public void generateFileDifferences(List<Artifact> endArtifacts,String diffPrefix,String nextParagraphNumber,String outlineType,boolean recurseChildren) throws OseeArgumentException, OseeCoreException {
  renderer.setOption("String_Node_Str",endArtifacts);
  renderer.setOption("String_Node_Str",nextParagraphNumber);
  renderer.setOption("String_Node_Str",outlineType);
  renderer.setOption("String_Node_Str",true);
  renderer.setOption("String_Node_Str",true);
  renderer.setOption("String_Node_Str",true);
  renderer.setOption("String_Node_Str",renderer.getBooleanOption(WordTemplateProcessor.PUBLISH_AS_DIFF));
  renderer.setOption(WordTemplateProcessor.PUBLISH_AS_DIFF,false);
  renderer.setOption("String_Node_Str",recurseChildren);
  BranchId endBranch=renderer.getBranchOption("String_Node_Str");
  renderer.setOption("String_Node_Str",endBranch);
  BranchId compareBranch=renderer.getBranchOption("String_Node_Str");
  TransactionToken startTransaction;
  if (compareBranch == null) {
    startTransaction=BranchManager.getBaseTransaction(endBranch);
    compareBranch=endBranch;
  }
 else {
    startTransaction=TransactionManager.getHeadTransaction(compareBranch);
  }
  TransactionToken endTransaction=TransactionManager.getHeadTransaction(endBranch);
  TransactionDelta txDelta;
  boolean maintainOrder=renderer.getBooleanOption("String_Node_Str");
  if (startTransaction.getId() < endTransaction.getId() || maintainOrder) {
    if (compareBranch.equals(endBranch)) {
      txDelta=new TransactionDelta(startTransaction,endTransaction);
    }
 else {
      txDelta=new TransactionDelta(endTransaction,startTransaction);
    }
  }
 else {
    txDelta=new TransactionDelta(startTransaction,endTransaction);
  }
  boolean recurseOnLoad=renderer.getBooleanOption(WordTemplateProcessor.RECURSE_ON_LOAD);
  Collection<Artifact> toProcess=recurseChildren || recurseOnLoad ? getAllArtifacts(endArtifacts) : endArtifacts;
  List<Change> changes=new LinkedList<>();
  ChangeDataLoader changeLoader=new ChangeDataLoader(changes,txDelta);
  IProgressMonitor monitor=(IProgressMonitor)renderer.getOption("String_Node_Str");
  if (monitor == null) {
    monitor=new NullProgressMonitor();
  }
  changeLoader.determineChanges(monitor);
  try {
    monitor.setTaskName("String_Node_Str");
    diff(changes,toProcess,diffPrefix,txDelta);
  }
 catch (  Exception ex) {
    OseeLog.log(Activator.class,Level.SEVERE,ex);
  }
}