Polish documentation
Update samples to use specific log configuration
Always reinitialize logging system

Update LoggingSystems so that they can reinitialize themselves
before logging begins. This allows reset of the root logger (which
may have been set to OFF in beforeInitialize) and also re-evaluation
of systems properties such as PID which may not have been set when
logging configuration was first loaded.

This commit may possibly reintroduce gh-1091, but it seems like
reloading is our only option.

Fixes gh-2125