Covering my plugin, stylesheet, and JS trails

Is there a way to make my Wordpress site not declare each and every plugin, stylesheet, and JS I have installed? I would like to make everything as non-Wordpress naming / neutral as possible. I would also like to get rid of the wp-config named directories if it will not break my shopping cart software. How does Etsy and PayPal manage to do this nowadays? Is there a set of plugins I can purchase from WPMUDEV to accomplish any / all of this? Thanks in advance...