On case-insensitive filesystems, git-merge deletes files that were recapitalized in another branch if rename detection fails. To repro: Run this script with git 1.8.4 on a case-insensitive filesystem. It repros for me on the default HFS filesystem on OS X 10.8, and also on Win7 NTFS. #!/bin/sh -x # create git repo git --version rm -rf caps git init caps cd caps git config --get core.ignorecase # commit empty file called "file" echo file > file git add . git commit -am "initial commit" # create branch called "branch" git branch branch # rename "file" to "File" # using --force per http://stackoverflow.com/questions/6899582 git mv --force file File echo "completely different content" > File git commit -am "renamed to File" # switch to branch, make a non-conflicting commit git checkout branch echo newfile > newfile git add . git commit -am "branch commit" # merge master into branch, commit merge git merge --verbose --commit --no-edit master ls File git status Actual: At the end of the script, the renamed File has been deleted by git-merge. "ls: File: No such file or directory" According to git-status, the deletion is not yet staged. Expected: There should be no untracked changes at the end of this script. The script runs as expected on Linux or case-sensitive HFS. -Dan Fabulich P.S. On case-insensitive HFS, git-init will automatically set core.ignorecase to true. For the sake of the experiment, I also tried setting core.ignorecase to false in the test repository. When I did that, I was unable to even checkout the "branch" branch without using --force. ("The following untracked working tree files would be overwritten by checkout: file" But git-status reported no untracked changes.) And then, once I did use force to switch to the branch, I was unable to merge from master at all. ("The following untracked working tree files would be overwritten by merge: File" But again, git-status reported no untracked changes.) -- To unsubscribe from this list: send the line "unsubscribe git" in the body of a message to majordomo@xxxxxxxxxxxxxxx More majordomo info at http://vger.kernel.org/majordomo-info.html