Hello, I have noticed an interesting interaction between git-diff-index and git-apply. Essentially, it seems that if we start with a clean working tree, then git-apply a patch, then git-apply the reverse of that patch, git-diff-index still thinks files are modified. But then, if we git-status, git-diff-index seems to "realize" the files are actually not modified. Below are steps to reproduce, as well as information about my machine, which I discovered this behavior on. Reproduction instructions: $ mkdir -p test/repo $ cd test/repo $ git init -q $ echo 1 > file $ git add file $ git commit -qm 1 $ echo 2 >> file $ git add file $ git commit -qm 2 $ git diff @~ > ../patch $ git apply --reverse ../patch $ git diff-index --name-only @ file $ git apply ../patch $ git diff-index --name-only @ file $ git status On branch master nothing to commit, working tree clean $ git diff-index --name-only @ $ echo hmm hmm System information: $ uname -a Darwin azdavis-mbp 16.3.0 Darwin Kernel Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64 i386 MacBookPro12,1 Darwin $ sw_vers ProductName: Mac OS X ProductVersion: 10.12.2 BuildVersion: 16C67 $ git --version git version 2.11.0 Thank you for your time. Ariel Davis