(#13429) refactor some settings initialization

This commit does the following:

• Move some of the settings initialization logic from Puppet::Util::CommandLine into the Puppet::Util::Settings class, so that it can be called by non-CommandLine code
• Rename / deprecate / clean up some methods related to parsing config files to try to promote a cleaner API for interacting with settings.
• Clean up / improve options for external tools to request puppet settings initialization.