Program: 185032
Project: 185032
Buggy source:
public static void parseInput(String filenameIn,String filenameOut) throws Exception {
  BufferedReader r=new BufferedReader(new FileReader(filenameIn));
  PrintWriter w=new PrintWriter(new FileWriter(filenameOut));
  if (r.ready()) {
    String numTestCasesLine=r.readLine();
    int numTestCases=Integer.parseInt(numTestCasesLine);
    for (int testCaseIndex=0; testCaseIndex < numTestCases; testCaseIndex++) {
      String testCaseLine=r.readLine();
      String[] testCaseInput=testCaseLine.split("String_Node_Str");
      int lineIndex=0;
      int numCombination=Integer.parseInt(testCaseInput[lineIndex++]);
      char[] combinationLookup=new char[257];
      for (int combinersIndex=0; combinersIndex < numCombination; combinersIndex++) {
        String combination=testCaseInput[lineIndex++];
        char base1=combination.charAt(0);
        char base2=combination.charAt(1);
        char result=combination.charAt(2);
        combinationLookup[baseLookup[base1] + baseLookup[base2]]=result;
      }
      int numOpposing=Integer.parseInt(testCaseInput[lineIndex++]);
      boolean[] opposingLookup=new boolean[257];
      for (int opposingIndex=0; opposingIndex < numOpposing; opposingIndex++) {
        String opossing=testCaseInput[lineIndex++];
        char base1=opossing.charAt(0);
        char base2=opossing.charAt(1);
        opposingLookup[baseLookup[base1] + baseLookup[base2]]=true;
      }
      int numInvokation=Integer.parseInt(testCaseInput[lineIndex++]);
      String invokation=testCaseInput[lineIndex++];
      String result="String_Node_Str";
      for (int invokationIndex=0; invokationIndex < numInvokation; invokationIndex++) {
        result+=invokation.charAt(invokationIndex);
        int resultLength=result.length();
        if (resultLength >= 2) {
          int lastElemValue=baseLookup[result.charAt(resultLength - 1)];
          int secondLastElemValue=baseLookup[result.charAt(resultLength - 2)];
          if (combinationLookup[lastElemValue + secondLastElemValue] != 0) {
            result=result.substring(0,resultLength - 2);
            result+=combinationLookup[lastElemValue + secondLastElemValue];
          }
 else {
            for (int resultIndex=0; resultIndex < resultLength; resultIndex++) {
              int currentElemValue=baseLookup[result.charAt(resultIndex)];
              if (currentElemValue != 0 && opposingLookup[lastElemValue + currentElemValue]) {
                result="String_Node_Str";
                break;
              }
            }
          }
        }
      }
      String outString="String_Node_Str" + (testCaseIndex + 1) + "String_Node_Str";
      outString+="String_Node_Str";
      int resultLength=result.length();
      for (int resultIndex=0; resultIndex < resultLength; resultIndex++) {
        outString+=result.charAt(resultIndex);
        if (resultIndex < resultLength - 1) {
          outString+="String_Node_Str";
        }
      }
      outString+="String_Node_Str";
      System.out.println(outString);
      w.println(outString);
    }
  }
  w.flush();
}

Fixed version (ground truth):
public static void parseInput(String filenameIn,String filenameOut) throws Exception {
  BufferedReader r=new BufferedReader(new FileReader(filenameIn));
  PrintWriter w=new PrintWriter(new FileWriter(filenameOut));
  if (r.ready()) {
    String numTestCasesLine=r.readLine();
    int numTestCases=Integer.parseInt(numTestCasesLine);
    for (int testCaseIndex=0; testCaseIndex < numTestCases; testCaseIndex++) {
      String testCaseLine=r.readLine();
      String[] testCaseInput=testCaseLine.split("String_Node_Str");
      int lineIndex=0;
      int numCombination=Integer.parseInt(testCaseInput[lineIndex++]);
      char[] combinationLookup=new char[257];
      for (int combinersIndex=0; combinersIndex < numCombination; combinersIndex++) {
        String combination=testCaseInput[lineIndex++];
        char base1=combination.charAt(0);
        char base2=combination.charAt(1);
        char result=combination.charAt(2);
        combinationLookup[baseLookup[base1] + baseLookup[base2]]=result;
      }
      int numOpposing=Integer.parseInt(testCaseInput[lineIndex++]);
      boolean[] opposingLookup=new boolean[257];
      for (int opposingIndex=0; opposingIndex < numOpposing; opposingIndex++) {
        String opossing=testCaseInput[lineIndex++];
        char base1=opossing.charAt(0);
        char base2=opossing.charAt(1);
        opposingLookup[baseLookup[base1] + baseLookup[base2]]=true;
      }
      int numInvokation=Integer.parseInt(testCaseInput[lineIndex++]);
      String invokation=testCaseInput[lineIndex++];
      String result="String_Node_Str";
      for (int invokationIndex=0; invokationIndex < numInvokation; invokationIndex++) {
        result+=invokation.charAt(invokationIndex);
        int resultLength=result.length();
        if (resultLength >= 2) {
          int lastElemValue=baseLookup[result.charAt(resultLength - 1)];
          int secondLastElemValue=baseLookup[result.charAt(resultLength - 2)];
          if (lastElemValue != 0 && secondLastElemValue != 0 && combinationLookup[lastElemValue + secondLastElemValue] != 0) {
            result=result.substring(0,resultLength - 2);
            result+=combinationLookup[lastElemValue + secondLastElemValue];
          }
 else {
            for (int resultIndex=0; resultIndex < resultLength; resultIndex++) {
              int currentElemValue=baseLookup[result.charAt(resultIndex)];
              if (currentElemValue != 0 && opposingLookup[lastElemValue + currentElemValue]) {
                result="String_Node_Str";
                break;
              }
            }
          }
        }
      }
      String outString="String_Node_Str" + (testCaseIndex + 1) + "String_Node_Str";
      outString+="String_Node_Str";
      int resultLength=result.length();
      for (int resultIndex=0; resultIndex < resultLength; resultIndex++) {
        outString+=result.charAt(resultIndex);
        if (resultIndex < resultLength - 1) {
          outString+="String_Node_Str";
        }
      }
      outString+="String_Node_Str";
      System.out.println(outString);
      w.println(outString);
    }
  }
  w.flush();
}