As @ErikEJ mentioned, you can use migrate.exe from the command line. Unfortunately (from the docs):
All the utility is designed to do is execute migrations. It cannot generate migrations or create a SQL script.
So you can run any existing migrations, but you can't create any new ones with this tool. That makes migrate.exe a pretty poor replacement for the tools EF provides in the Package Manager Explorer.
I tried manually importing the EntityFramework.psd1 file in the Package Manager Console:
PM> Import-Module ".\packages\EntityFramework\tools\EntityFramework.psd1"
While this made the Enable-Migrations command available, running it produced the following error:
No packages installed.
The EntityFramework package is not installed on project 'Foo'.
I'm guessing that this is all going to work better with EF7. But for now, it looks like I'll either have to ditch paket altogether, or have a frankenstein of both Paket and Nuget to get this working.