This lifts logging options to the bootstrap stage in order to be able
to configure logging before plugins are loaded.  The logging setup is
lifted out from GoalRunner to a top-level function in the logging
package and tests are added for logging configuration.

Additionally, bootstrap option parsing is fixed to handle short flags
since logging uses a few of these.

Document the difference between bootstrap and global options.
Explicitly enable the 'WARN' alias for logging at 'WARNING' level.
Fix a bug where passthrough options with the same name as bootstrap
options would be bootstrapped.

…rois/logging/early_setup