Applying for PHD in Europe: getting a recommendation
I have no experience applying to German institutions, but I have applied to programs in the US, Norway, Netherlands.  My answer is based of those experiences.

If the program you are applying to does not specify that you provide recommendations, don't put them in your application.  If the committee thinks you are a strong candidate, and they want a recommendation, they will ask for it.  It is entirely expected however, that you should be able to present at least two strong recommendations upon request, in which case you provide their email and phone number in the application.

Since you have both academic and industry experience, it would be valuable to represent both.  Email your supervisor from the University you attended and ask them if he/she can provide a strong recommendation for you.  Briefly summarize what your research included just to help refresh their memory.  It never hurts to mention why you enjoyed your research and why you are inspired to get a PhD.

Good luck!