(maint) Enable logging for all `puppet doc` commands

Without this commit the --debug and --verbose flags can only be used
with the rdoc mode and doesn't interact with the other documentation
types. This commit extracts the logging configuration to apply to all
documentation modes.

In addition this defaults the log level to :warning. Since warning and
above messages will be emitted on stderr this will not affect the normal
operation of the `puppet doc` command. Using --debug or --verbose will
emit messages on stdout, so they should not be used while
programmatically generating docs.