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Only reproducible on Windows b/c of different path separator. On a windows machine, issue:

> mkdir foo bar
> touch foo\__init__.py foo\spam.py bar\__init__.py bar\eggs.py
> stubgen foo\spam.py bar\eggs.py

Result: stubgen never finishes, because caught in the endless while loop: out\foo/ doesn't start with out\bar/, then doesn't start with out/, then with / repeatedly.

Since mypy supports only Python 3.5 and onwards anyway - may I suggest using pathlib instead of string manipulation? With pathlib, the task of finding the common parent directory is a walk in the park and works on all OSes. For example, the common_dir_prefix method could look like this:

from pathlib import Path

def common_dir_prefix(paths: List[str]) -> str:
    if not paths:
        return '.'
    cur = Path(paths[0])
    for parent in cur.parents:
        # if the parent is parent of all paths, we're good to go
        if all(parent in Path(path).parents for path in paths[1:]):
            return str(parent)
    return '.'

In addition, if an extensive path manipulation is done in mypy (didn't check that), I would also plead switching to pathlib exclusively.