Modified ConsoleReader to use System.in instead of FileDescriptor.in. Big thanks to escortkeel for the (unfortunately very old) PR.

src/main/java/net/minecraft/server/MinecraftServer.java

@@ -15,6 +15,7 @@ import java.util.logging.Logger;
 
 // CraftBukkit start
 import java.io.PrintStream;
+import java.io.PrintWriter;
 import java.net.UnknownHostException;
 import jline.ConsoleReader;
 import joptsimple.OptionSet;
@@ -82,7 +83,7 @@ public class MinecraftServer implements Runnable, ICommandListener, IMinecraftSe
         // CraftBukkit start
         this.options = options;
         try {
-            this.reader = new ConsoleReader();
+            this.reader = new ConsoleReader(System.in, new PrintWriter(System.out)); // CraftBukkit - Added "System.in, new PrintWriter(System.out)" in the constuctor
         } catch (IOException ex) {
             Logger.getLogger(MinecraftServer.class.getName()).log(Level.SEVERE, null, ex);
         }