Remove deprecations from core

In progress. Feel free to take bits of it if you'd like.

### TODO

* [ ] Remove `Point.translate` calls, use `Point.add`? See `text-editor-spec` and `text-editor-component-spec`, @nathansobo a while ago, I swapped `add` for `translate` and specs were failing. 
* [ ] Use checkpoints rather than transactions? See `text-editor-spec` and `text-editor-component-spec`. @nathansobo or @maxbrunsfeld 
* [ ] Upgrade the theme manager specs. Several events are asking for using something on atom.styles. Not sure if we want to test these or suppress. @nathansobo this is your domain.