Misc fixes and tweaks

Two fixes:

  - Change Gemfile source to 'https://rubygems.org' so that bundler will quit whining.

  - Initialize `unlink_empty_files` to `false` instead of `nil`.

And a new feature:

  - Allow `filetype` to be specified as a class attribute that controls which FileType class is used to interact with the file system instead of always defaulting to `:flat`.