Hi Manuel,
The packages (repos) rasa_core and rasa_nlu were merged in the new package rasa starting with version 1.0, which is the one you have installed with version 1.3.9. The rasa package is of course not designed to work with older versions of core or nlu and I doubt it would give good results.
Regarding your main issue: projects feature was removed in 1.0 and there are currently no plans to reintroduce it (see the discussions here Removing projects · Issue #3259 · RasaHQ/rasa · GitHub and here Removing projects for Rasa NLU server).