Well, I added more qube colors with qubesd-query, that’s simple, but how do I make corresponding icons to make everything look right?
I’m curious so I searched in the Qubes-OS repositories.
Seems to be done in qubes-desktop-linux-common by appicons_create() with qubesimgconverter.tint().
See also the qvm-get-tinted-image command, the colour argument tints the image.
So now you need to follow the appicons_create() calls to understand the full image creation workfkow… Good luck 
Try qvm-appmenus --update <VMNAME>.
Seems like a wrong place to me: it is how the system creates the colorized version of appmenu icons, but the cube icons are created elsewhere. the “colors” bash script uses imagemagick’s “convert” command to draw ugly rectangles, but it sucks.
I gave it one more shot and found out that actually no, pre-colored icons are just rasterized from SVG there, there is no way to add more colors with this script. 
anyone has an idea how to do it properly?