Respect initialLine and initialColumn options when reopening a file

Alright, first things first: Atom is awesome!

Second, I’m not completely happy with my pull request. I’ve used the patched Atom for two weeks - the problem seems to be fixed.

But.

It seems that [this line](https://github.com/alexandershov/atom/commit/229e7e03b2e7ad3f89ddb1e43ee2d237f6c754b7#diff-88caa33888e5345667751ee7182b4c36R459) works correctly (meaning "setting new cursor position and scrolling to it") only if it's placed after the code doing the pane creation/activation. It still works, but I have a hunch that programming by coincidence isn't a good practice ;)

Also, I couldn’t find specs for AtomApplication, which means that [this change](https://github.com/alexandershov/atom/commit/229e7e03b2e7ad3f89ddb1e43ee2d237f6c754b7#diff-9929202e800354a2caa775ed44c61bfeR362) is not covered by tests.

So, getting some advice from a smart person would be cool.

This variable doesn't seem to be used