Program: 179003
Project: 179003
Buggy source:
private void userInit(PlayerJoinEvent event){
  SlowMode slow=SlowMode.getInstance();
  ViewableInventory.replInv((CraftPlayer)event.getPlayer());
  User user=User.getUser(event.getPlayer());
  String cheatstring="String_Node_Str";
  if (!user.hasPerm("String_Node_Str")) {
    cheatstring+="String_Node_Str";
    cheatstring+="String_Node_Str";
  }
  if (!user.hasPerm("String_Node_Str")) {
    cheatstring+="String_Node_Str";
    cheatstring+="String_Node_Str";
    cheatstring+="String_Node_Str";
  }
  if (!cheatstring.isEmpty()) {
    cheatstring=cheatstring.replaceAll("String_Node_Str","String_Node_Str");
    user.sendMessage(cheatstring);
  }
  if (BenCmd.updateAvailable && user.hasPerm("String_Node_Str")) {
    user.sendMessage(ChatColor.RED + "String_Node_Str");
  }
  Player[] playerList=Bukkit.getOnlinePlayers();
  if (user.hasPerm("String_Node_Str")) {
    if (playerList.length == 1) {
      user.sendMessage(ChatColor.GREEN + "String_Node_Str");
    }
 else {
      String playerString="String_Node_Str";
      for (      Player player2 : playerList) {
        if (User.getUser(player2).isOffline()) {
          continue;
        }
        playerString+=User.getUser(player2).getColor() + player2.getDisplayName() + ChatColor.WHITE+ "String_Node_Str";
      }
      user.sendMessage("String_Node_Str" + playerString);
    }
  }
  if (user.isMuted() != null) {
    user.sendMessage(ChatColor.RED + "String_Node_Str");
  }
 else   if (slow.isEnabled()) {
    user.sendMessage(ChatColor.RED + "String_Node_Str" + (slow.getDefTime() / 1000)+ "String_Node_Str");
  }
  if (user.hasPerm("String_Node_Str") && BenCmd.getReports().unreadTickets()) {
    user.sendMessage(ChatColor.RED + "String_Node_Str");
  }
  if (BenCmd.getChatChannels().getChannel(user.getVar("String_Node_Str","String_Node_Str")) != null) {
    user.joinChannel(BenCmd.getChatChannels().getChannel(user.getVar("String_Node_Str","String_Node_Str")),false);
  }
  event.setJoinMessage(user.getColor() + user.getDisplayName() + ChatColor.YELLOW+ "String_Node_Str");
  if (BenCmd.getPermissionManager().getActionFile().isUnjailed(user) != null) {
    user.spawn();
    BenCmd.getPermissionManager().getActionFile().removeAction(BenCmd.getPermissionManager().getActionFile().isUnjailed(user));
  }
  if (user.isJailed() != null) {
    user.warpTo(BenCmd.getPermissionManager().getJailWarp());
  }
  if (user.isDev()) {
    ((Player)user.getHandle()).getWorld().strikeLightningEffect(((Player)user.getHandle()).getLocation());
    Bukkit.broadcastMessage(ChatColor.DARK_GREEN + "String_Node_Str");
  }
}

Fixed version (ground truth):
private void userInit(PlayerJoinEvent event){
  SlowMode slow=SlowMode.getInstance();
  ViewableInventory.replInv((CraftPlayer)event.getPlayer());
  User user=User.getUser(event.getPlayer());
  String cheatstring="String_Node_Str";
  if (!user.hasPerm("String_Node_Str")) {
    cheatstring+="String_Node_Str";
    cheatstring+="String_Node_Str";
  }
  if (!user.hasPerm("String_Node_Str")) {
    cheatstring+="String_Node_Str";
    cheatstring+="String_Node_Str";
    cheatstring+="String_Node_Str";
  }
  if (!cheatstring.isEmpty()) {
    cheatstring=cheatstring.replaceAll("String_Node_Str","String_Node_Str");
    user.sendMessage(cheatstring);
  }
  if (BenCmd.updateAvailable && user.hasPerm("String_Node_Str")) {
    user.sendMessage(ChatColor.RED + "String_Node_Str");
  }
  Player[] playerList=Bukkit.getOnlinePlayers();
  if (user.hasPerm("String_Node_Str")) {
    if (playerList.length == 1) {
      user.sendMessage(ChatColor.GREEN + "String_Node_Str");
    }
 else {
      String playerString="String_Node_Str";
      for (      Player player2 : playerList) {
        if (User.getUser(player2).isOffline()) {
          continue;
        }
        playerString+=User.getUser(player2).getColor() + player2.getDisplayName() + ChatColor.WHITE+ "String_Node_Str";
      }
      user.sendMessage("String_Node_Str" + playerString);
    }
  }
  if (user.isMuted() != null) {
    user.sendMessage(ChatColor.RED + "String_Node_Str");
  }
 else   if (slow.isEnabled()) {
    user.sendMessage(ChatColor.RED + "String_Node_Str" + (slow.getDefTime() / 1000)+ "String_Node_Str");
  }
  if (user.hasPerm("String_Node_Str") && BenCmd.getReports().unreadTickets()) {
    user.sendMessage(ChatColor.RED + "String_Node_Str");
  }
  if (BenCmd.getChatChannels() != null) {
    if (BenCmd.getChatChannels().getChannel(user.getVar("String_Node_Str","String_Node_Str")) != null) {
      user.joinChannel(BenCmd.getChatChannels().getChannel(user.getVar("String_Node_Str","String_Node_Str")),false);
    }
  }
  event.setJoinMessage(user.getColor() + user.getDisplayName() + ChatColor.YELLOW+ "String_Node_Str");
  if (BenCmd.getPermissionManager().getActionFile().isUnjailed(user) != null) {
    user.spawn();
    BenCmd.getPermissionManager().getActionFile().removeAction(BenCmd.getPermissionManager().getActionFile().isUnjailed(user));
  }
  if (user.isJailed() != null) {
    user.warpTo(BenCmd.getPermissionManager().getJailWarp());
  }
  if (user.isDev()) {
    ((Player)user.getHandle()).getWorld().strikeLightningEffect(((Player)user.getHandle()).getLocation());
    Bukkit.broadcastMessage(ChatColor.DARK_GREEN + "String_Node_Str");
  }
}