Indeed, Paglen's been great on this. See also his Cabinet article http://www.cabinetmagazine.org/issues/24/paglen.php which goes beyond NRO to other beloved organizations (e.g. "a secret Air Force Base near Groom Lake).
My best friend's Dad was a Nasa Engineer and would always bring back packs of NASA launch stickers for the neighborhood kids. This reminds me a lot of those.
Some of those had some really cool designs like the ones in the story.
I was confused, too. My default interpretation of "patch" is a file for modifying an existing binary. Second place goes to the swatch of material used to repair holes in fabric or plastic. The last time I thought of the kind of patch the article was referencing, it was for my scout uniform.
To upgrade to version 1.1 of the repair material for the embroidered insignia, you will need a patch patch patch.
Machines for making those are now widely available. TechShop has CNC embroidery machines.