Update the behavior of close-current to be 'replace' the current window.

This fixes #16 and #5.

Now this *does* work, but I know the implementation is ridiculous. I sunk into the source code of atom for awhile and realized that an atom instance doesn't like change (most functions refer to a state that was created from a query string on initial load). 

I'm going to continue using this fork locally as it improves my experience significantly but I'm creating this pull request mainly as a documented example to reference in https://github.com/atom/atom/issues/2818