Program: 34414
Project: 34414
Buggy source:
static String populateProjectData(NewModuleProjectData data,String paths,boolean assignValues){
  if (data.getProjectName() != null && data.getCodeNameBase() != null && assignValues) {
    return null;
  }
  String wrongOnes=null;
  StringTokenizer tokens=new StringTokenizer(paths,File.pathSeparator);
  boolean cutShortestPath=false;
  boolean fileAlreadyMarked=false;
  if (tokens.hasMoreTokens()) {
    fileAlreadyMarked=false;
    File fil=new File(tokens.nextToken());
    if (!fil.exists()) {
      return wrongOnes;
    }
    String name=fil.getName();
    int inddd=name.lastIndexOf('.');
    if (inddd > -1) {
      name=name.substring(0,inddd);
    }
    name=name.replaceAll("String_Node_Str","String_Node_Str");
    if (assignValues) {
      data.setProjectName(name);
    }
    JarFile jf=null;
    String shortestPath=null;
    try {
      jf=new JarFile(fil);
      if (assignValues) {
        Manifest manifest=jf.getManifest();
        Attributes attributes=manifest.getMainAttributes();
        if (attributes.getValue("String_Node_Str") != null) {
          data.setProjectName(attributes.getValue("String_Node_Str").replaceAll("String_Node_Str","String_Node_Str").replaceAll("String_Node_Str","String_Node_Str"));
        }
 else {
          if (manifest.getEntries().size() == 1) {
            attributes=manifest.getEntries().values().iterator().next();
            if (attributes.getValue("String_Node_Str") != null) {
              data.setProjectName(attributes.getValue("String_Node_Str").replaceAll("String_Node_Str","String_Node_Str").replaceAll("String_Node_Str","String_Node_Str"));
            }
          }
        }
      }
      Enumeration en=jf.entries();
      while (en.hasMoreElements()) {
        JarEntry entry=(JarEntry)en.nextElement();
        if (!entry.isDirectory() && entry.getName().endsWith("String_Node_Str")) {
          String nm=entry.getName();
          if (!ApisupportAntUtils.isValidJavaFQN(nm.substring(0,nm.length() - 6).replace('/','.'))) {
            continue;
          }
          int index=nm.lastIndexOf('/');
          if (index > -1) {
            String path=nm.substring(0,index);
            if (shortestPath != null && path.length() == shortestPath.length() && !path.equals(shortestPath)) {
              cutShortestPath=true;
            }
            if (shortestPath == null || path.length() < shortestPath.length()) {
              shortestPath=path;
              cutShortestPath=false;
            }
          }
 else {
            if (!fileAlreadyMarked) {
              wrongOnes=wrongOnes == null ? fil.getName() : wrongOnes + "String_Node_Str" + fil.getName();
              fileAlreadyMarked=true;
            }
          }
        }
      }
    }
 catch (    IOException e) {
      ErrorManager.getDefault().notify(ErrorManager.WARNING,e);
    }
 finally {
      if (jf != null) {
        try {
          jf.close();
        }
 catch (        IOException e) {
          Util.err.notify(ErrorManager.INFORMATIONAL,e);
        }
      }
    }
    if (shortestPath != null && assignValues) {
      shortestPath=shortestPath.replace('/','.');
      if (cutShortestPath && shortestPath.indexOf('.') != shortestPath.lastIndexOf('.')) {
        int ind=shortestPath.lastIndexOf('.');
        shortestPath=shortestPath.substring(0,ind);
      }
      data.setCodeNameBase(shortestPath);
    }
  }
  return wrongOnes;
}

Fixed version (ground truth):
static String populateProjectData(NewModuleProjectData data,String paths,boolean assignValues){
  if (data.getProjectName() != null && data.getCodeNameBase() != null && assignValues) {
    return null;
  }
  String wrongOnes=null;
  StringTokenizer tokens=new StringTokenizer(paths,File.pathSeparator);
  boolean cutShortestPath=false;
  boolean fileAlreadyMarked=false;
  if (tokens.hasMoreTokens()) {
    fileAlreadyMarked=false;
    File fil=new File(tokens.nextToken());
    if (!fil.exists()) {
      return wrongOnes;
    }
    String name=fil.getName();
    int inddd=name.lastIndexOf('.');
    if (inddd > -1) {
      name=name.substring(0,inddd);
    }
    name=name.replaceAll("String_Node_Str","String_Node_Str");
    if (assignValues) {
      data.setProjectName(name);
    }
    JarFile jf=null;
    String shortestPath=null;
    try {
      jf=new JarFile(fil);
      if (assignValues) {
        Manifest manifest=jf.getManifest();
        if (manifest != null) {
          Attributes attributes=manifest.getMainAttributes();
          if (attributes.getValue("String_Node_Str") != null) {
            data.setProjectName(attributes.getValue("String_Node_Str").replaceAll("String_Node_Str","String_Node_Str").replaceAll("String_Node_Str","String_Node_Str"));
          }
 else {
            if (manifest.getEntries().size() == 1) {
              attributes=manifest.getEntries().values().iterator().next();
              if (attributes.getValue("String_Node_Str") != null) {
                data.setProjectName(attributes.getValue("String_Node_Str").replaceAll("String_Node_Str","String_Node_Str").replaceAll("String_Node_Str","String_Node_Str"));
              }
            }
          }
        }
      }
      Enumeration en=jf.entries();
      while (en.hasMoreElements()) {
        JarEntry entry=(JarEntry)en.nextElement();
        if (!entry.isDirectory() && entry.getName().endsWith("String_Node_Str")) {
          String nm=entry.getName();
          if (!ApisupportAntUtils.isValidJavaFQN(nm.substring(0,nm.length() - 6).replace('/','.'))) {
            continue;
          }
          int index=nm.lastIndexOf('/');
          if (index > -1) {
            String path=nm.substring(0,index);
            if (shortestPath != null && path.length() == shortestPath.length() && !path.equals(shortestPath)) {
              cutShortestPath=true;
            }
            if (shortestPath == null || path.length() < shortestPath.length()) {
              shortestPath=path;
              cutShortestPath=false;
            }
          }
 else {
            if (!fileAlreadyMarked) {
              wrongOnes=wrongOnes == null ? fil.getName() : wrongOnes + "String_Node_Str" + fil.getName();
              fileAlreadyMarked=true;
            }
          }
        }
      }
    }
 catch (    IOException e) {
      ErrorManager.getDefault().notify(ErrorManager.WARNING,e);
    }
 finally {
      if (jf != null) {
        try {
          jf.close();
        }
 catch (        IOException e) {
          Util.err.notify(ErrorManager.INFORMATIONAL,e);
        }
      }
    }
    if (shortestPath != null && assignValues) {
      shortestPath=shortestPath.replace('/','.');
      if (cutShortestPath && shortestPath.indexOf('.') != shortestPath.lastIndexOf('.')) {
        int ind=shortestPath.lastIndexOf('.');
        shortestPath=shortestPath.substring(0,ind);
      }
      data.setCodeNameBase(shortestPath);
    }
  }
  return wrongOnes;
}