We solve this by creating a schema definition for mongo collections, from within the app layer. Now we have easy version control where we want it, not in sqldump files like we used to. That was painful.
Most full stack frameworks have a way to create migrations. When the schema changes over time, you just get a mess with mongo, thats just my observation. Its far easier to manage change with db migrations.
You'd be right except that we also have the ability to create data migrations based on schema changes over time. I'm glad it's not built into MongoDB or else we wouldn't have the (fairly ideal) solution we built to work with it today.