This was really good!
I feel like constructing and effectively balancing this sort of game within a short timeframe is a significant challenge, and for the most part, this pulls it off.
I felt uncertain of how some enemies were intended to be approached, and found myself very fragile to some of the faster enemies, resulting in my preferring to pick everybody off from a distance. Don't think that's necessarily bad gameplay, but I don't feel like the level design or weapon design is really leading toward that.
The upgrade system is cool, and even though I managed to defeat the boss after level 3 (after many attempts :D ), I don't feel like I saw them all.
Your Linux binary did not have executable permissions, and your jam page didn't include instructions on setting them via chmod. If it's helpful at all, I made a tool that allows Windows users to manage Unix style executable permissions.