The CommandAPI has support to use Minecraft's functions within your plugins. This is handled by using a class provided by the CommandAPI called FunctionWrapper, which allows you to execute functions. The CommandAPI also provides support to let you run your own commands within Minecraft function files.

In order to use a command from your plugin in a .mcfunction file, you must register your command in your plugin's onLoad() method, instead of the onEnable() method. Failure to do so will not allow the command to be registered for Minecraft functions, causing the function file to fail to load during the server startup phase.

Developer's Note:

In short, if you want to register a command which can be used in Minecraft functions, register it in your plugin's onLoad() method.

public class Main extends JavaPlugin {

    @Override
    public void onLoad() {
        //Commands which will be used in Minecraft functions are registered here

        CommandAPI.getInstance().register("killall", new LinkedHashMap<>(), (sender, args) -> {
            //Kills all enemies in all worlds
            Bukkit.getWorlds()
                .forEach(w -> w.getLivingEntities()
                    .forEach(e -> e.setHealth(0))
                );
        });
    }
    
    @Override
    public void onEnable() {
        //Register all other commands here
    } 
}