Without looking carefully yet, I think I like your cleanup of freeze_modules.py, but not the rename of the deepfreeze directory. Can you undo the latter and just focus on improving the script?

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.

Looks good for this phase! I'll merge this now. Then you can work on e.g. changes groups of functions to classes and partially freezing encodings.