The bibliography no longer compiles on Linux

We are writing our bachelor's thesis using this template. The bibliography was working fine. Suddenly, all citations and references became undefined when we compiled. It literally happened over the weekend. I cloned an old working version of our thesis and it still wouldn't compile. I cloned this repository and tried to compile the example documents and it still wouldn't work. It complains that the .bbl file is missing. I have no idea were to begin to debug this.