checkout: don't remove other links when checking out particular dvc file

[efiop]

Currently dvc checkout(and dvc pull) improperly collect all stages to remove unused links. When a target is specified, links are collected only for target stages https://github.com/iterative/dvc/blob/0.32.1/dvc/repo/checkout.py#L27 and then all other links are removed https://github.com/iterative/dvc/blob/0.32.1/dvc/repo/checkout.py#L31 , which is not correct.