Keep bower_components and vendor separate.

This ensures that `import Baz from 'bower_components/foo-bar/baz';` works properly. Prior to this change you would have had to know and understand that we are internally merging `bower_components/` and `vendor/` together (and therefore you would need to use `import Baz from 'vendor/foo-bar/baz';`).

No fundamental functionality was lost, but it might be a breaking change for folks that were importing things that happened to be in `bower_components/`, but were using `vendor/` in the import.  I'll make sure to call it out as a breaking change in the changelog.

Addresses #1789, in that `app.import('bower_components/foo-bar/baz.js')` and `import Foo from 'bower_components/foo-bar/baz';` now show the proper directories in the errors that spit out.