Test Environment Just Boots up Mod-less Minecraft

When I boot up the good ol' test environment, nothing from my mod is anywhere to be seen. Not in the Mods menu on the title screen, not in the Creative inventory, and not even in /give. The only way for me to test my mod at the moment is to export the whole thing and put it in my .minecraft folder (which is 10x more of a pain).

Is this an issue with the application itself, or is there some setting that got changed unintentionally when I upgraded from 1.9.0 to 1.9.1? It's a pretty pressing issue...