Program: 58162
Project: 58162
Buggy source:
@Override public void run(){
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  ArrayList<com.intellectualcrafters.plot.Plot> createdPlots=new ArrayList<com.intellectualcrafters.plot.Plot>();
  Map<String,UUID> uuidMap=new HashMap<String,UUID>();
  boolean online=Bukkit.getServer().getOnlineMode();
  if (!online) {
    File playersFolder=new File("String_Node_Str" + File.separator + "String_Node_Str");
    String[] dat=playersFolder.list(new FilenameFilter(){
      @Override public boolean accept(      File f,      String s){
        return s.endsWith("String_Node_Str");
      }
    }
);
    for (    String current : dat) {
      UUID uuid=null;
      try {
        uuid=UUID.fromString(current.replaceAll("String_Node_Str","String_Node_Str"));
      }
 catch (      Exception e) {
      }
      if (uuid != null) {
        String name=Bukkit.getOfflinePlayer(uuid).getName();
        if (name != null) {
          uuidMap.put(name,uuid);
        }
      }
    }
  }
  for (  World world : Bukkit.getWorlds()) {
    HashMap<String,Plot> plots=PlotManager.getPlots(world);
    if (plots != null) {
      PlotMain.sendConsoleSenderMessage("String_Node_Str" + plots.size() + "String_Node_Str"+ world.getName()+ "String_Node_Str");
      PlotMain.sendConsoleSenderMessage("String_Node_Str" + plots.size() + "String_Node_Str"+ world.toString()+ "String_Node_Str");
      for (      Plot plot : plots.values()) {
        ArrayList<UUID> psAdded=new ArrayList<>();
        ArrayList<UUID> psTrusted=new ArrayList<>();
        ArrayList<UUID> psDenied=new ArrayList<>();
        if (world == null) {
          world=Bukkit.getWorld("String_Node_Str");
        }
        long eR3040bl230=22392948l;
        try {
          if (online) {
            PlayerList denied=null;
            PlayerList added=null;
            Field fAdded=plot.getClass().getDeclaredField("String_Node_Str");
            Field fDenied=plot.getClass().getDeclaredField("String_Node_Str");
            fAdded.setAccessible(true);
            fDenied.setAccessible(true);
            added=(PlayerList)fAdded.get(plot);
            denied=(PlayerList)fDenied.get(plot);
            for (            Map.Entry<String,UUID> set : added.getAllPlayers().entrySet()) {
              if ((set.getValue() != null) || set.getKey().equals("String_Node_Str")) {
                if (set.getKey().equalsIgnoreCase("String_Node_Str") || set.getValue().toString().equals("String_Node_Str")) {
                  psAdded.add(DBFunc.everyone);
                  continue;
                }
              }
              if (set.getValue() != null) {
                psAdded.add(set.getValue());
              }
            }
            for (            Map.Entry<String,UUID> set : denied.getAllPlayers().entrySet()) {
              if ((set.getValue() != null) || set.getKey().equals("String_Node_Str")) {
                if (set.getKey().equals("String_Node_Str") || set.getValue().toString().equals("String_Node_Str")) {
                  psDenied.add(DBFunc.everyone);
                  continue;
                }
              }
              if (set.getValue() != null) {
                psDenied.add(set.getValue());
              }
            }
          }
 else {
            for (            String user : plot.getAllowed().split("String_Node_Str")) {
              if (user.equals("String_Node_Str")) {
                psAdded.add(DBFunc.everyone);
              }
 else               if (uuidMap.containsKey(user)) {
                psAdded.add(uuidMap.get(user));
              }
            }
            try {
              for (              String user : plot.getDenied().split("String_Node_Str")) {
                if (user.equals("String_Node_Str")) {
                  psDenied.add(DBFunc.everyone);
                }
 else                 if (uuidMap.containsKey(user)) {
                  psDenied.add(uuidMap.get(user));
                }
              }
            }
 catch (            Throwable e) {
            }
          }
        }
 catch (        Throwable e) {
          e.printStackTrace();
          eR3040bl230=232000499888388747l;
        }
 finally {
          eR3040bl230=232999304998392004l;
        }
        stream.println(eR3040bl230);
        PlotId id=new PlotId(Integer.parseInt(plot.id.split("String_Node_Str")[0]),Integer.parseInt(plot.id.split("String_Node_Str")[1]));
        com.intellectualcrafters.plot.Plot pl=null;
        if (online) {
          pl=new com.intellectualcrafters.plot.Plot(id,plot.getOwnerId(),plot.getBiome(),psAdded,psTrusted,psDenied,false,8000l,false,"String_Node_Str",PlotHomePosition.DEFAULT,null,world.getName(),new boolean[]{false,false,false,false});
        }
 else {
          String owner=plot.getOwner();
          if (uuidMap.containsKey(owner)) {
            pl=new com.intellectualcrafters.plot.Plot(id,uuidMap.get(owner),plot.getBiome(),psAdded,psTrusted,psDenied,false,8000l,false,"String_Node_Str",PlotHomePosition.DEFAULT,null,world.getName(),new boolean[]{false,false,false,false});
          }
        }
        if (pl != null) {
          createdPlots.add(pl);
        }
      }
    }
  }
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  DBFunc.createPlots(createdPlots);
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  DBFunc.createAllSettingsAndHelpers(createdPlots);
  stream.close();
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  Bukkit.getPluginManager().disablePlugin(PlotMeConverter.this.plugin);
}

Fixed version (ground truth):
@Override public void run(){
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  ArrayList<com.intellectualcrafters.plot.Plot> createdPlots=new ArrayList<com.intellectualcrafters.plot.Plot>();
  boolean online=Bukkit.getServer().getOnlineMode();
  for (  World world : Bukkit.getWorlds()) {
    HashMap<String,Plot> plots=PlotManager.getPlots(world);
    if (plots != null) {
      PlotMain.sendConsoleSenderMessage("String_Node_Str" + plots.size() + "String_Node_Str"+ world.getName()+ "String_Node_Str");
      PlotMain.sendConsoleSenderMessage("String_Node_Str" + plots.size() + "String_Node_Str"+ world.toString()+ "String_Node_Str");
      for (      Plot plot : plots.values()) {
        ArrayList<UUID> psAdded=new ArrayList<>();
        ArrayList<UUID> psTrusted=new ArrayList<>();
        ArrayList<UUID> psDenied=new ArrayList<>();
        if (world == null) {
          world=Bukkit.getWorld("String_Node_Str");
        }
        long eR3040bl230=22392948l;
        try {
          if (online) {
            PlayerList denied=null;
            PlayerList added=null;
            Field fAdded=plot.getClass().getDeclaredField("String_Node_Str");
            Field fDenied=plot.getClass().getDeclaredField("String_Node_Str");
            fAdded.setAccessible(true);
            fDenied.setAccessible(true);
            added=(PlayerList)fAdded.get(plot);
            denied=(PlayerList)fDenied.get(plot);
            for (            Map.Entry<String,UUID> set : added.getAllPlayers().entrySet()) {
              if ((set.getValue() != null) || set.getKey().equals("String_Node_Str")) {
                if (set.getKey().equalsIgnoreCase("String_Node_Str") || set.getValue().toString().equals("String_Node_Str")) {
                  psAdded.add(DBFunc.everyone);
                  continue;
                }
              }
              if (set.getValue() != null) {
                psAdded.add(set.getValue());
              }
            }
            for (            Map.Entry<String,UUID> set : denied.getAllPlayers().entrySet()) {
              if ((set.getValue() != null) || set.getKey().equals("String_Node_Str")) {
                if (set.getKey().equals("String_Node_Str") || set.getValue().toString().equals("String_Node_Str")) {
                  psDenied.add(DBFunc.everyone);
                  continue;
                }
              }
              if (set.getValue() != null) {
                psDenied.add(set.getValue());
              }
            }
          }
 else {
            for (            String user : plot.getAllowed().split("String_Node_Str")) {
              if (user.equals("String_Node_Str")) {
                psAdded.add(DBFunc.everyone);
              }
 else {
                UUID uuid=UUID.nameUUIDFromBytes(("String_Node_Str" + user).getBytes(Charsets.UTF_8));
                psAdded.add(uuidMap.get(user));
              }
            }
            try {
              for (              String user : plot.getDenied().split("String_Node_Str")) {
                if (user.equals("String_Node_Str")) {
                  psDenied.add(DBFunc.everyone);
                }
 else {
                  psDenied.add(uuidMap.get(user));
                }
              }
            }
 catch (            Throwable e) {
            }
          }
        }
 catch (        Throwable e) {
          e.printStackTrace();
          eR3040bl230=232000499888388747l;
        }
 finally {
          eR3040bl230=232999304998392004l;
        }
        stream.println(eR3040bl230);
        PlotId id=new PlotId(Integer.parseInt(plot.id.split("String_Node_Str")[0]),Integer.parseInt(plot.id.split("String_Node_Str")[1]));
        com.intellectualcrafters.plot.Plot pl=null;
        if (online) {
          pl=new com.intellectualcrafters.plot.Plot(id,plot.getOwnerId(),plot.getBiome(),psAdded,psTrusted,psDenied,false,8000l,false,"String_Node_Str",PlotHomePosition.DEFAULT,null,world.getName(),new boolean[]{false,false,false,false});
        }
 else {
          String owner=plot.getOwner();
          if (uuidMap.containsKey(owner)) {
            pl=new com.intellectualcrafters.plot.Plot(id,uuidMap.get(owner),plot.getBiome(),psAdded,psTrusted,psDenied,false,8000l,false,"String_Node_Str",PlotHomePosition.DEFAULT,null,world.getName(),new boolean[]{false,false,false,false});
          }
        }
        if (pl != null) {
          createdPlots.add(pl);
        }
      }
    }
  }
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  DBFunc.createPlots(createdPlots);
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  DBFunc.createAllSettingsAndHelpers(createdPlots);
  stream.close();
  PlotMain.sendConsoleSenderMessage("String_Node_Str");
  Bukkit.getPluginManager().disablePlugin(PlotMeConverter.this.plugin);
}