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This is great. I have a few nits.

I also wonder if there aren't more improvements we can make, e.g. use relative paths throughout the code, rather than computing absolute paths and then making them relative for the generated code again.

Oh, and it would be nice to be able to freeze some submodules in a package but not all of them -- e.g. I'd like to freeze encodings/{__init__,utf_8,aliases}.py but not the remaining 100 submodules in that package.