On OS X using whatever filesystem it comes with by default, I get the 
following, which doesn't seem right (but in a different way).

$ 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
$ git add FOO
$ git commit -m case\ change
$ ls
FOO bar
$ git pull . side
Trying really trivial in-index merge...
fatal: Merge requires file-level merging
Nope.
Merging HEAD with e1f1e78035b099fad2bbfb82af7ec31864d8e4c1
Merging: 
5d70969775bf595dd5144a2bacc25d32cc288352 case change 
e1f1e78035b099fad2bbfb82af7ec31864d8e4c1 side commit 
found 1 common ancestor(s): 
e35c42fad4f08c2ccf61d93409a0208e92028a51 initial commit 

Merge 98bf1cae75776c141ad3b61dc2cb938c71c303ef, made by recursive.
 bar |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)
$ 
$ ls
bar
$ git ls-files -d
FOO
$ git ls-tree HEAD
100644 blob b7d6715e2df11b9c32b2341423273c6b3ad9ae8a    FOO
100644 blob 5f8b81e197a2cb27816112fb5a6b86b7031ffde8    bar

The checkout is losing the FOO file but the merged tree object has the 
merged FOO in it.

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