Program: 17784
Project: 17784
Buggy source:
public void performPopupMenu(final Object source){
  if (source == this.popupFileRefresh || source == this.popupRefreshItem || source == this.popupFileCSVRefresh || source == popupRootRefreshItem) {
    EncogWorkBench.getInstance().getMainWindow().getTree().refresh();
  }
 else   if (source == this.popupRootNewFile) {
    try {
      CreateNewFile.performCreateFile();
    }
 catch (    IOException e) {
      EncogWorkBench.displayError("String_Node_Str",e);
    }
  }
  boolean first=true;
  List<ProjectItem> list=this.owner.getTree().getSelectedValue();
  if (list == null)   return;
  for (  ProjectItem selected : list) {
    if (source == this.popupFileDelete) {
      if (first && !EncogWorkBench.askQuestion("String_Node_Str","String_Node_Str")) {
        return;
      }
      first=false;
      if (selected instanceof ProjectFile) {
        ((ProjectFile)selected).getFile().delete();
      }
      EncogWorkBench.getInstance().getMainWindow().getTree().refresh();
    }
 else     if (source == this.popupFileOpen || source == this.popupFileCSVOpen) {
      if (selected instanceof ProjectFile) {
        EncogWorkBench.getInstance().getMainWindow().openFile(((ProjectFile)selected).getFile());
      }
    }
 else     if (source == this.popupFileOpenText) {
      if (selected instanceof ProjectFile) {
        EncogWorkBench.getInstance().getMainWindow().openTextFile(((ProjectFile)selected).getFile());
      }
    }
 else     if ((source == this.popupNetworkDelete) || (source == this.popupDataDelete) || (source == this.popupGeneralDelete)|| (source == this.popupFileCSVDelete)) {
      if (first && !EncogWorkBench.askQuestion("String_Node_Str","String_Node_Str")) {
        return;
      }
      owner.getOperations().performObjectsDelete(selected);
    }
 else     if (source == this.popupFileCSVExport) {
      String sourceFile=((ProjectFile)selected).getFile().toString();
      String targetFile=FileUtil.forceExtension(sourceFile,"String_Node_Str");
      ImportExport.performExternal2Bin(new File(sourceFile),new File(targetFile),null);
    }
 else     if (source == this.popupFileCSVWizard) {
      File sourceFile=((ProjectFile)selected).getFile();
      EncogAnalystWizard.createEncogAnalyst(sourceFile);
    }
    first=false;
  }
}

Fixed version (ground truth):
public void performPopupMenu(final Object source){
  if (source == this.popupFileRefresh || source == this.popupRefreshItem || source == this.popupFileCSVRefresh || source == popupRootRefreshItem) {
    EncogWorkBench.getInstance().getMainWindow().getTree().refresh();
  }
 else   if (source == this.popupRootNewFile) {
    try {
      CreateNewFile.performCreateFile();
    }
 catch (    IOException e) {
      EncogWorkBench.displayError("String_Node_Str",e);
    }
  }
  boolean first=true;
  List<ProjectItem> list=this.owner.getTree().getSelectedValue();
  if (list == null)   return;
  for (  ProjectItem selected : list) {
    if (source == this.popupFileDelete || source == this.popupFileCSVDelete || source == this.popupDataDelete || source == this.popupGeneralDelete) {
      if (first && !EncogWorkBench.askQuestion("String_Node_Str","String_Node_Str")) {
        return;
      }
      first=false;
      if (selected instanceof ProjectFile) {
        ((ProjectFile)selected).getFile().delete();
      }
      EncogWorkBench.getInstance().getMainWindow().getTree().refresh();
    }
 else     if (source == this.popupFileOpen || source == this.popupFileCSVOpen) {
      if (selected instanceof ProjectFile) {
        EncogWorkBench.getInstance().getMainWindow().openFile(((ProjectFile)selected).getFile());
      }
    }
 else     if (source == this.popupFileOpenText) {
      if (selected instanceof ProjectFile) {
        EncogWorkBench.getInstance().getMainWindow().openTextFile(((ProjectFile)selected).getFile());
      }
    }
 else     if ((source == this.popupNetworkDelete) || (source == this.popupDataDelete) || (source == this.popupGeneralDelete)|| (source == this.popupFileCSVDelete)) {
      if (first && !EncogWorkBench.askQuestion("String_Node_Str","String_Node_Str")) {
        return;
      }
      owner.getOperations().performObjectsDelete(selected);
    }
 else     if (source == this.popupFileCSVExport) {
      String sourceFile=((ProjectFile)selected).getFile().toString();
      String targetFile=FileUtil.forceExtension(sourceFile,"String_Node_Str");
      ImportExport.performExternal2Bin(new File(sourceFile),new File(targetFile),null);
    }
 else     if (source == this.popupFileCSVWizard) {
      File sourceFile=((ProjectFile)selected).getFile();
      EncogAnalystWizard.createEncogAnalyst(sourceFile);
    }
    first=false;
  }
}