Very simple to reproduce on FAT and NTFS, and under Windows, as usual, when a problem is especially annoying. I seem to have no chance to get my hands on this myself, so I at least let everyone know about the problem. The case goes as follows: $ mkdir case-sensitivity-test $ cd case-sensitivity-test $ git init-db defaulting to local storage area $ echo foo > foo $ echo bar > bar $ git add foo bar $ git commit -m initial\ commit Committing initial tree 89ff1a2aefcbff0f09197f0fd8beeb19a7b6e51c $ git checkout -b side $ echo bar-side >> bar $ git commit -m side\ commit -o bar $ git checkout master $ rm foo $ git update-index --remove foo $ echo FOO > FOO # note case change $ git add FOO # this is on linux, vfat on an usbstick (mounted with default case # conversion, which is "lower". That's why the file can't be found). # Have no Windows at home. On Windows the FOO is created and "git add" # just passes. We just assume it did add the file, as it would there. git-ls-files: error: pathspec 'FOO' did not match any. Maybe you misspelled it? $ git commit -m case\ change $ git pull . side Trying really trivial in-index merge... git-read-tree: fatal: Untracked working tree file 'foo' would be overwritten by merge. Nope. Really trivial in-index merge is not possible. Merging HEAD with 7b0cad3a104487fa92afa06736294338acb84281 Merging: 7f6a8ba3e41683ef5b55921d050092e766aad4a5 case change 7b0cad3a104487fa92afa06736294338acb84281 side commit found 1 common ancestor(s): f857aaf5f1d3716d25ca7751f12de30420d9b2aa initial commit git-read-tree: git-read-tree: fatal: Untracked working tree file 'foo' would be overwritten by merge. No merge strategy handled the merge. Well, what now? What I did was to replace that die() with error() in read-tree.c:verify_absent, which if cause is not acceptable. I'll try to find a solution sometime later, but I really hope someone will find it sooner (because it'll take some time for me). Hope it didn't bit anyone yet... - : 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