Program: 24507
Project: 24507
Buggy source:
public void onMessage(String channel,String sender,String login,String hostname,String message){
  if (message.trim().startsWith(pref)) {
    message=message.replaceFirst(Matcher.quoteReplacement(pref),"String_Node_Str");
    String[] parts=message.split("String_Node_Str");
    String first=parts[0];
    String result="String_Node_Str";
    for (int i=1; i < parts.length; i++) {
      if (result.length() != 0)       result+="String_Node_Str";
      result+=parts[i];
    }
    if ((first.equalsIgnoreCase(("String_Node_Str")) || message.equalsIgnoreCase("String_Node_Str")) && sender.equalsIgnoreCase("String_Node_Str")) {
      System.exit(0);
    }
 else     if (first.equalsIgnoreCase("String_Node_Str")) {
      try {
        System.out.println("String_Node_Str");
        Main.reLoad();
        System.out.println("String_Node_Str");
        Main.bot.sendMessage(channel,"String_Node_Str");
      }
 catch (      Throwable e) {
        e.printStackTrace();
      }
    }
 else     if (first.equalsIgnoreCase("String_Node_Str")) {
      String toprint="String_Node_Str";
      if (Main.helpmap.containsKey(result)) {
        toprint=Main.helpmap.get(result);
      }
 else {
        for (        Map.Entry<String,String> entry : Main.helpmap.entrySet()) {
          toprint+=entry.getKey();
        }
      }
      Main.bot.sendMessage(channel,toprint);
    }
 else     if (Main.cmdmap.containsKey(first)) {
      try {
        Method met=(Method)Main.cmdmap.get(first);
        met.invoke((BasePlugin)Main.classmap.get(first),channel,sender,login,hostname,result);
      }
 catch (      Throwable e) {
        e.printStackTrace();
      }
    }
  }
}

Fixed version (ground truth):
public void onMessage(String channel,String sender,String login,String hostname,String message){
  if (message.trim().startsWith(pref)) {
    message=message.replaceFirst(Matcher.quoteReplacement(pref),"String_Node_Str");
    String[] parts=message.split("String_Node_Str");
    String first=parts[0];
    String result="String_Node_Str";
    for (int i=1; i < parts.length; i++) {
      if (result.length() != 0)       result+="String_Node_Str";
      result+=parts[i];
    }
    if ((first.equalsIgnoreCase(("String_Node_Str")) || message.equalsIgnoreCase("String_Node_Str")) && sender.equalsIgnoreCase("String_Node_Str")) {
      System.exit(0);
    }
 else     if (first.equalsIgnoreCase("String_Node_Str")) {
      try {
        System.out.println("String_Node_Str");
        Main.reLoad();
        System.out.println("String_Node_Str");
        Main.bot.sendMessage(channel,"String_Node_Str");
      }
 catch (      Throwable e) {
        e.printStackTrace();
      }
    }
 else     if (first.equalsIgnoreCase("String_Node_Str")) {
      String toprint="String_Node_Str";
      if (Main.helpmap.containsKey(result)) {
        toprint=Main.helpmap.get(result);
      }
 else {
        for (        Map.Entry<String,String> entry : Main.helpmap.entrySet()) {
          toprint+=entry.getKey() + "String_Node_Str";
        }
      }
      Main.bot.sendMessage(channel,toprint.trim());
    }
 else     if (Main.cmdmap.containsKey(first)) {
      try {
        Method met=(Method)Main.cmdmap.get(first);
        met.invoke((BasePlugin)Main.classmap.get(first),channel,sender,login,hostname,result);
      }
 catch (      Throwable e) {
        e.printStackTrace();
      }
    }
  }
}