Replace cerr with cout where not necessary

[mad-de]

cerr potentially interferes with accessing scripts which are differentiating between cout and cerr outputs (such as mine :( )

[nh2]

This would be great to have, I also suffer somewhat from stderr being spammed.

The PR looks good to me, the only thing that should be fixed is the 3 added cases of cout << "Usage followed by exit(1). Those should be stderr, because they are actual errors.