Simple class for changing Minecraft server properties easily.

Properties.java

import org.bukkit.Bukkit;

import java.lang.reflect.InvocationTargetException;

public class Properties {

    public static void savePropertiesFile() throws Exception {
        Object propertyManager = getPropertyManager( getMinecraftServer() );
        propertyManager.getClass().getDeclaredMethod( "savePropertiesFile" ).invoke( propertyManager );
    }

    public static void setServerProperty(ServerProperty property, Object value) throws Exception {
        Object propertyManager = getPropertyManager( getMinecraftServer() );
        propertyManager.getClass().getDeclaredMethod( "setProperty", String.class, Object.class ).invoke( propertyManager, property.getPropertyName(), value );
    }

    public enum ServerProperty {

        SPAWN_PROTECTION("spawn-protection"),
        SERVER_NAME("server-name"),
        FORCE_GAMEMODE("force-gamemode"),
        NETHER("allow-nether"),
        DEFAULT_GAMEMODE("gamemode"),
        QUERY("enable-query"),
        PLAYER_IDLE_TIMEOUT("player-idle-timeout"),
        DIFFICULTY("difficulty"),
        SPAWN_MONSTERS("spawn-monsters"),
        OP_PERMISSION_LEVEL("op-permission-level"),
        RESOURCE_PACK_HASH("resource-pack-hash"),
        RESOURCE_PACK("resource-pack"),
        ANNOUNCE_PLAYER_ACHIEVEMENTS("announce-player-achievements"),
        PVP("pvp"),
        SNOOPER("snooper-enabled"),
        LEVEL_NAME("level-name"),
        LEVEL_TYPE("level-type"),
        LEVEL_SEED("level-seed"),
        HARDCORE("hardcore"),
        COMMAND_BLOCKS("enable-command-blocks"),
        MAX_PLAYERS("max-players"),
        PACKET_COMPRESSION_LIMIT("network-compression-threshold"),
        MAX_WORLD_SIZE("max-world-size"),
        IP("server-ip"),
        PORT("server-port"),
        DEBUG_MODE("debug"),
        SPAWN_NPCS("spawn-npcs"),
        SPAWN_ANIMALS("spawn-animals"),
        FLIGHT("allow-flight"),
        VIEW_DISTANCE("view-distance"),
        WHITE_LIST("white-list"),
        GENERATE_STRUCTURES("generate-structures"),
        MAX_BUILD_HEIGHT("max-build-height"),
        MOTD("motd"),
        REMOTE_CONTROL("enable-rcon");

        private String propertyName;

        ServerProperty(String propertyName) {
            this.propertyName = propertyName;
        }

        public String getPropertyName() {
            return propertyName;
        }

    }

    public static String getVersion() {
        return Bukkit.getServer().getClass().getPackage().getName().split("\\.")[3];
    }

    public static Object getMinecraftServer() throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException {
        return Class.forName( "net.minecraft.server." + getVersion() + ".MinecraftServer" ).getDeclaredMethod("getServer").invoke( null );
    }

    public static Object getPropertyManager( Object minecraftServer ) throws ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException {
        if(!Class.forName( "net.minecraft.server." + getVersion() + ".MinecraftServer" ).isInstance( minecraftServer )) {
            throw new IllegalArgumentException( "The supplied object isn't a minecraft server." );
        }
        return minecraftServer.getClass().getDeclaredMethod( "getPropertyManager" ).invoke( minecraftServer );
    }

}