Reduce the amount of warning to a feasible minimum and documented those which stay

In 5.12.1 on Linux desktop, Neptune from the installer posts 13 warnings on a plain startup on the console. This amount of warnings might be taken as a sign of low quality or undocumented issues.

I wish this amount will be reduced before the release 5.13 to a lowest possible minimum. Those warnings which have to stay should be included in the documentation with an explanation why they are coming.