FactionChat

package me.superckl.addonmanager.commands;

import me.superckl.addonmanager.AddonManagerPlugin;

import com.massivecraft.factions.Conf;
import com.massivecraft.factions.cmd.FCommand;
import com.massivecraft.factions.struct.ChatMode;
import com.massivecraft.factions.struct.Permission;

/**
 * 'Borrowed' from Factions and editted a bit
 */
public class FactionChat extends FCommand{

	  public FactionChat()
	  {
	    this.aliases.add("c");
	    this.aliases.add("chat");

	    this.optionalArgs.put("mode", "next");

	    this.permission = Permission.CHAT.node;
	    this.disableOnLock = false;

	    this.senderMustBePlayer = true;
	    this.senderMustBeMember = true;
	    this.senderMustBeModerator = false;
	    this.senderMustBeAdmin = false;
	  }

	  public void perform()
	  {
	    if (!Conf.factionOnlyChat)
	    {
	      msg("<b>The built in chat chat channels are disabled on this server.", new Object[0]);
	      return;
	    }

	    String modeString = argAsString(0);
	    ChatMode modeTarget = this.fme.getChatMode().getNext();

	    if (modeString != null)
	    {
	      modeString.toLowerCase();
	      if (modeString.startsWith("p"))
	      {
	        modeTarget = ChatMode.PUBLIC;
	      }
	      else if (modeString.startsWith("a"))
	      {
	        modeTarget = ChatMode.ALLIANCE;
	      }
	      else if (modeString.startsWith("f"))
	      {
	        modeTarget = ChatMode.FACTION;
	      }
	      else
	      {
	        msg("<b>Unrecognised chat mode. <i>Please enter either 'a','f' or 'p'", new Object[0]);
	        return;
	      }
	    }

	    this.fme.setChatMode(modeTarget);
	    AddonManagerPlugin.getUser(this.me.getName()).setChatMode(modeTarget);
	    if (this.fme.getChatMode() == ChatMode.PUBLIC)
	    {
	      msg("<i>Public chat mode.", new Object[0]);
	    }
	    else if (this.fme.getChatMode() == ChatMode.ALLIANCE)
	    {
	      msg("<i>Alliance only chat mode.", new Object[0]);
	    }
	    else
	    {
	      msg("<i>Faction only chat mode.", new Object[0]);
	    }
	  }
}

Overriding a Factions subcommand

		try {
			Field field = MPlugin.class.getDeclaredField("baseCommands");
			field.setAccessible(true);
			((List<MCommand<?>>)field.get(Bukkit.getPluginManager().getPlugin("Factions"))).get(0).subCommands.set(4, new FactionChat());
		} catch (IllegalArgumentException | IllegalAccessException
				| NoSuchFieldException | SecurityException e) {
			e.printStackTrace();
		}