It seems that in #285 you made it so that when a tool like yapf formats code inline pre-commit will always mark the check as failed, because files were changed. Is this correct?

If so, funnily enough the behaviour I'm looking for is the exact thing you felt was a "fix". I'd like this to be able to pass:

[WARNING] Unstaged files detected.
[INFO] Stashing unstaged files to /Users/jasonkuhrt/.cache/pre-commit/patch1525490932.
yapf.....................................................................Failed
hookid: yapf

Files were modified by this hook.

[INFO] Restored changes from /Users/jasonkuhrt/.cache/pre-commit/patch1525490932.

I suppose that would require pre-commit to stage the auto formatted changes automatically too.

Any chance of supporting this? Its how pretty-quick works for example.