There is a command-line program Valve includes with the SDK called bspzip. It's command line though. So, to remedy it, there are some skins, including PakRat, which is a very common one to use.
Yep. I'm a total noob, and I just used Pakrat the other day to put some custom textures I found on this site into my .bsp when I wanted a friend to take a look at it. It has an auto feature that tries to find all the custom files and adds them for you, then you get to look at what it added and see if it's to your liking before you pack it up. Worked like a charm for me, no sweat.
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