I‘d argue that a single db should be handled by a single set of migrations. And if you don‘t follow that advice then you want to avoid dependencies between the separate systems. That can be done e.g. using namespacing of global things like tables.
One could argue that migrations should run in order of the dependency tree between the applications, but not sure if ecto does/could have access to that.
Edit: Maybe you can already customize the oder with the ecto_repos configuration.
