Git pull silently removing files in the index

Question

I think there's a bug in git pull. Doing a git pull in a fresh repository without any commits removes files in the index.

Example:

$ mkdir foo
$ cd foo
$ git init
$ touch file1 file2
$ git add file1
$ ls
file1 file2
$ git pull https://github.com/sos4nt/empty.git master
$ ls
file2

"file2" is still there, but "file1" was silently removed and no error message was shown.

I'm running git 1.8.3.1