cloaked links html and nofollow

Hi

In the root of my domain are all different .html files each containing a cloaked javascript affiliate link. So in the article it will point to example.com/myproduct.html or example.com/thisproduct.html

Then it opens in a new page for the user with the title as per the link name. Now i have 2 questions?

1) do i still need the "nofollow" tag if so does it need to go within the file or on the end of the link code in wordpress
2) would i be better putting the html files into a folder e.g. /out and modifying my robots.txt so they aren`t indexed

thanks
Coco

1. you just need the nofollow inside the php code
2. yes better to put inside separate folder and block it so it will not be discovered by googlebots