daemon: Let all command line options override global options from the config.

daemon: Let all command line options override global options from the config.

This replaces 09fb81e130ad70bf0547cec3d3c349ce8cb092cf which provided a
specific solution for the `PIDFile' option. The new solution is generic and
more nicely abstracted without the need for global variables across multiple
modules.

Fixes #366