Program: 18374
Project: 18374
Buggy source:
protected String getOriginalReplacement(String[] baseCases,int caseId,String prefix){
  StringBuffer result=new StringBuffer();
  if (caseId >= baseCases.length)   throw new RuntimeException("String_Node_Str" + caseId);
  String[] prefixes=new String[baseCases.length];
  for (int i=0; i < baseCases.length; i++) {
    prefixes[i]=prefixes[i] + "String_Node_Str";
    String baseCase=baseCases[i].replaceAll("String_Node_Str","String_Node_Str").trim();
    if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]="String_Node_Str";
      baseCase=baseCase.substring(7);
    }
 else     if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]="String_Node_Str";
      baseCase=baseCase.substring(8);
    }
 else     if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]="String_Node_Str";
      baseCase=baseCase.substring(10);
    }
    if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]=prefixes[i] + "String_Node_Str";
      baseCase=baseCase.substring(9);
    }
 else     if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]=prefixes[i] + "String_Node_Str";
      baseCase=baseCase.substring(16);
    }
 else     if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]=prefixes[i] + "String_Node_Str";
      baseCase=baseCase.substring(21);
    }
    baseCases[caseId]=baseCase;
  }
  System.out.println("String_Node_Str" + baseCases[caseId]);
  Pattern p=Pattern.compile("String_Node_Str",Pattern.DOTALL);
  Matcher m=p.matcher(baseCases[caseId]);
  while (m.find()) {
    for (int i=2; i <= m.groupCount(); i++) {
      StringBuilder sb=new StringBuilder(baseCases[caseId]);
      sb.setCharAt(m.start(i),'�');
      baseCases[caseId]=sb.toString();
    }
    System.out.println("String_Node_Str" + baseCases[caseId]);
  }
  String[] clausesA=baseCases[caseId].trim().split("String_Node_Str");
  boolean append=false;
  for (int i=0; i < clausesA.length; i++) {
    if (clausesA[i].trim().startsWith(prefix + "String_Node_Str")) {
      result.append("String_Node_Str" + clausesA[i].trim().replaceFirst(prefix,"String_Node_Str") + "String_Node_Str");
      result.append("String_Node_Str");
      append=true;
    }
  }
  if (append)   result.setLength(result.length() - 4);
  return result.toString().replaceAll("String_Node_Str","String_Node_Str");
}

Fixed version (ground truth):
protected String getOriginalReplacement(String[] baseCases,int caseId,String prefix){
  StringBuffer result=new StringBuffer();
  if (caseId >= baseCases.length)   throw new RuntimeException("String_Node_Str" + caseId);
  String[] prefixes=new String[baseCases.length];
  for (int i=0; i < baseCases.length; i++) {
    prefixes[i]=prefixes[i] + "String_Node_Str";
    String baseCase=baseCases[i].replaceAll("String_Node_Str","String_Node_Str").trim();
    if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]="String_Node_Str";
      baseCase=baseCase.substring(7);
    }
 else     if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]="String_Node_Str";
      baseCase=baseCase.substring(8);
    }
 else     if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]="String_Node_Str";
      baseCase=baseCase.substring(10);
    }
    if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]=prefixes[i] + "String_Node_Str";
      baseCase=baseCase.substring(9);
    }
 else     if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]=prefixes[i] + "String_Node_Str";
      baseCase=baseCase.substring(16);
    }
 else     if (baseCase.startsWith("String_Node_Str")) {
      prefixes[i]=prefixes[i] + "String_Node_Str";
      baseCase=baseCase.substring(21);
    }
    baseCases[caseId]=baseCase;
  }
  System.out.println("String_Node_Str" + baseCases[caseId]);
  Pattern p=Pattern.compile("String_Node_Str",Pattern.DOTALL);
  Matcher m=p.matcher(baseCases[caseId]);
  while (m.find()) {
    for (int i=2; i <= m.groupCount(); i++) {
      StringBuilder sb=new StringBuilder(baseCases[caseId]);
      sb.setCharAt(m.start(i),'�');
      baseCases[caseId]=sb.toString();
    }
    m=p.matcher(baseCases[caseId]);
    System.out.println("String_Node_Str" + baseCases[caseId]);
  }
  String[] clausesA=baseCases[caseId].trim().split("String_Node_Str");
  boolean append=false;
  for (int i=0; i < clausesA.length; i++) {
    if (clausesA[i].trim().startsWith(prefix + "String_Node_Str")) {
      result.append("String_Node_Str" + clausesA[i].trim().replaceFirst(prefix,"String_Node_Str") + "String_Node_Str");
      result.append("String_Node_Str");
      append=true;
    }
  }
  if (append)   result.setLength(result.length() - 4);
  return result.toString().replaceAll("String_Node_Str","String_Node_Str");
}