Put all output from kalite manage setup in log

[benjaoming]

Summary

Some of the output during setup is just added via print statements and sys.stderr, we should log everything the proper way so it goes into server.log.

System information

All systems

Real-life consequences (anything community should be aware, for instance how it affects your deployment)

It's hard to properly debug problems pertaining initial setup. Currently, we have an issue with certificates, and it's impossible to tell if they've been generated or not.

[benjaoming]

Fixed in #5441