> Could there perhaps be a way to input additional 
urls that do not pop up on the auto-generated 
index.html in the project folder?> 
> For example, say a website has a hidden link or 
something similar -- a link that is not linked to 
anywhere but part of the same site.  I wouldn't mind 
getting both with the same file, but is there any way 
to prevent HTTrack from adding the second URL to the 
index?
Well, yes : include all URLs you want to hide in the 
URL list, and then select the url list among with the 
URLs types in the URL box. These URLs won't appear in 
the index, normally!