Fix cascade problem with site.baseurl.

[parkr]

Problem described in #931. This is a fix for it.

[brainkim]

What a coincidence! I was digging around the code and saw this problem while mapping out the options and how they transform/cascade throughout the program (it's complex). The problem is that any defaults we define with commander will always override Jekyll::DEFAULTS as well as _config.yml, which is how Jekyll.configuration was initially designed. My recommendation (I am not a committer so take this with a grain of salt) would be to move all the Commander defaults except :serving to Jekyll::DEFAULTS so that we have them all in one place and don't have any surprising behavior/discrepancies. Removing baseurl won't be enough because we've also lost the ability to set the port and host using _config.yml. :serving currently makes the build and serve commands play nice but could also be refactored out as well.

[parkr]

@mojombo would like to keep all options in Jekyll::DEFAULTS.