Tests: test_logging again passes all tests
Corrected overzealousness in shared configuration variable initialization

Commit 3268e72f51b22e0780ef0f74f90d7bb9f5d610a1 created a shared
configuration variable initialization function, init_shared_cfg_vars(),
which was intended to initialize configuration variables shared between
Core and the CGIs. The function went too far and initialized some things
that are not configuration variables and caused problems (like preventing
daemon mode). This commit corrects that overzealousness.