Typeshed uses the @python2 subdirectory for Python 2 variants of stubs. Mypy could also support this convention for custom search paths. This would make dealing with mixed Python 2/3 codebases a little easier.
If there is a user-defined mypy search path directory foo, first look for files under foo/@python2 when type checking in Python 2 mode. Ignore @python2 directories in Python 3 mode. We should still look into foo as well if a module is not found under the @python2 subdirectory.
This should work with mypy_path in a config file and the MYPYPATH environment variable. This is mostly useful with stubs, but this would work will regular Python files as well.