Untested, but wouldn't affect anyone who wasn't already messed up

src/main/java/co/aikar/commands/ACFPatterns.java

@@ -45,7 +45,6 @@ final class ACFPatterns {
     public static final Pattern INTEGER = Pattern.compile("^[0-9]+$");
     public static final Pattern VALID_NAME_PATTERN = Pattern.compile("^[a-zA-Z0-9_-]{2,16}$");
     public static final Pattern NON_PRINTABLE_CHARACTERS = Pattern.compile("[^\\x20-\\x7F]");
-
     public static final Pattern EQUALS = Pattern.compile("=");
 
 

src/main/java/co/aikar/commands/BukkitCommandManager.java

@@ -25,9 +25,12 @@ package co.aikar.commands;
 
 import co.aikar.timings.lib.TimingManager;
 import org.bukkit.Bukkit;
+import org.bukkit.Location;
 import org.bukkit.Server;
 import org.bukkit.command.Command;
+import org.bukkit.command.CommandException;
 import org.bukkit.command.CommandMap;
+import org.bukkit.command.CommandSender;
 import org.bukkit.command.SimpleCommandMap;
 import org.bukkit.event.EventHandler;
 import org.bukkit.event.Listener;
@@ -59,9 +62,13 @@ public class BukkitCommandManager extends CommandManager {
             Method getCommandMap = server.getClass().getDeclaredMethod("getCommandMap");
             getCommandMap.setAccessible(true);
             commandMap = (CommandMap) getCommandMap.invoke(server);
-            if (!commandMap.getClass().equals(SimpleCommandMap.class)) {
+            if (!SimpleCommandMap.class.isAssignableFrom(commandMap.getClass())) {
                 ACFLog.severe("ERROR: CommandMap has been hijacked! Offending command map is located at: " + commandMap.getClass().getName());
-                ACFLog.severe("Commands are most likely broken unless the hijacker did it in a friendly way.");
+                ACFLog.severe("We are going to try to hijack it back and resolve this, but you are now in dangerous territory.");
+                ACFLog.severe("We can not guarantee things are going to work.");
+                Field cmField = server.getClass().getDeclaredField("commandMap");
+                cmField.set(server, new ProxyCommandMap(commandMap));
+                ACFLog.info("Injected Proxy Command Map... good luck...");
             }
             Field knownCommands = commandMap.getClass().getDeclaredField("knownCommands");
             knownCommands.setAccessible(true);
@@ -154,4 +161,79 @@ public class BukkitCommandManager extends CommandManager {
     public TimingManager getTimings() {
         return timingManager;
     }
+
+    class ProxyCommandMap extends SimpleCommandMap {
+
+        CommandMap proxied;
+
+        ProxyCommandMap(CommandMap proxied) {
+            super(Bukkit.getServer());
+            this.proxied = proxied;
+        }
+
+        @Override
+        public void registerAll(String fallbackPrefix, List<Command> commands) {
+            proxied.registerAll(fallbackPrefix, commands);
+        }
+
+        @Override
+        public boolean register(String label, String fallbackPrefix, Command command) {
+            if (isOurCommand(command)) {
+                return super.register(label, fallbackPrefix, command);
+            } else {
+                return proxied.register(label, fallbackPrefix, command);
+            }
+        }
+
+        boolean isOurCommand(String cmdLine) {
+            String[] args = ACFPatterns.SPACE.split(cmdLine);
+            return args.length != 0 && isOurCommand(knownCommands.get(args[0].toLowerCase(Locale.ENGLISH)));
+
+        }
+        boolean isOurCommand(Command command) {
+            return command instanceof BaseCommand && ((BaseCommand) command).manager == BukkitCommandManager.this;
+        }
+
+        @Override
+        public boolean register(String fallbackPrefix, Command command) {
+            if (isOurCommand(command)) {
+                return super.register(fallbackPrefix, command);
+            } else {
+                return proxied.register(fallbackPrefix, command);
+            }
+        }
+
+        @Override
+        public boolean dispatch(CommandSender sender, String cmdLine) throws CommandException {
+            if (isOurCommand(cmdLine)) {
+                return super.dispatch(sender, cmdLine);
+            } else {
+                return proxied.dispatch(sender, cmdLine);
+            }
+        }
+
+        @Override
+        public void clearCommands() {
+            super.clearCommands();;
+            proxied.clearCommands();
+        }
+
+        @Override
+        public Command getCommand(String name) {
+            if (isOurCommand(name)) {
+                return super.getCommand(name);
+            } else {
+                return proxied.getCommand(name);
+            }
+        }
+
+        @Override
+        public List<String> tabComplete(CommandSender sender, String cmdLine) throws IllegalArgumentException {
+            if (isOurCommand(cmdLine)) {
+                return super.tabComplete(sender, cmdLine);
+            } else {
+                return proxied.tabComplete(sender, cmdLine);
+            }
+        }
+    }
 }