I had one of the companions,Vilkas, as a follower. I got tired of his gear so I spent a large some of money plus my saved dragon bones and scales to build his very own dragon gear, with shield. Their all legendary so the gear is at the max. We went to fought off a bunch of bandits near markarth and right after completing the quest we head on back to markarth to collect the bounty. After I dismissed him we left Understone. Right after we came outside he had on his original gear! How is that possible when I took all of his gear away?

Obviously this code, Removeallitems, is not permanent so I was wondering what is the code to permanently delete a NPC followers inventory so they cannot wear their original gear again?

I'm not sure there's really a way to do that. If you search around, you'll see that a lot of people have this issue and HAVE had since the game released. Now, there's a mod to make sure that spouses use the clothing you give them; there may be a mod for followers out there too - I just haven't run into it.... and I don't use followers (or have spouses) so I haven't gone looking really.

If you dismiss a follower and then rehire him/her later, he/she will respawn a new set of default gear and ignore any gear you left in inventory. It's just one of the infuriating follower bugs (along with the improper leveling, mismatches between gear and combat skills with some of them, etc.) that has yet to be addressed in a patch.

You'll need to re-use the removeallitems command on him to get rid of his default kit, and every time you dismiss and then rehire him again.