What You WIll Need:
Notepad (or any other text editor, whichever you prefer)

That's all, really.

First, navigate to ...Steam\steamapps\common\Cortex Command/W40K.rte/Weapons. Now pop open Weapon Index.ini with your text editor of choice.

You can disable/hide a weapon in the load order by commenting its line out- just add two slashes (//) to the start of a line.

You can change the position of an item in the load order simply by moving it. Basically, what you see in the list there is what you'll see in the shop list.

Let's say I don't want to see any of the basic Autoweapons in the load order. Simple enough. I just find every stub/auto weapon, and prefix their lines with a double-slash. Save the file, fire up CC, and bam - no stub/auto weapons in the list.

There are a couple of alternate weapon index files already provided, one of which groups weapons by type rather than category (bolt/plasma/melta vs pistols/rifles/heavy). You can easily use these by renaming the base weapon index to something else, and then renaming the one you want to use to just "Weapon Index.ini".

Just remember that disabling certain weapons will probably break compatibility with certain scenarios - particularly Void Wanderers and Unmapped Lands 2.