give access to default configurations directly off of prototype
adding plugin initiation logic
instantiate plugins with instance as parameter
Merge branch 'pluginPrep' of https://github.com/hdngr/Alchemy into hdngr-pluginPrep

Conflicts:
	app/index.html
	app/scripts/alchemy/Alchemy.coffee.md
Merge branch 'release-0.4.1' of https://github.com/GraphAlchemist/Alchemy into release-0.4.1