This has several benefits: changes are isolated - easier to reason about and track in version control system, refactoring is easier.
Programmers are just about the last people who work with filesystems directly. I expect git will be used for sharing for a while, but I wonder what it will take to move beyond checking out code into local working directories to a more cloud notebook-style approach? (There are lots of experiments but it's not mainstream.)
I've been thinking about a source control system, that will track functions/classes, instead of bytes. You could track who changed that helper method and not be distracted by moving classes between files.