Stage files, then remote add, then pull - and my files are gone
$ git status
# On branch master
nothing to commit (working directory clean)

$ git reflog
c80135d HEAD@{0}: checkout: moving from 999d128ea4e6969f9eacbceebb5f857f2aa5abb0 to master
999d128 HEAD@{1}: checkout: moving from master to HEAD~1
c80135d HEAD@{2}: checkout: moving from 999d128ea4e6969f9eacbceebb5f857f2aa5abb0 to master
999d128 HEAD@{3}: checkout: moving from master to 999d128ea4e6969f9eacbceebb5f857f2aa5abb0
c80135d HEAD@{4}: commit (amend): updated ignore
28b4f90 HEAD@{5}: commit: updated ignore
999d128 HEAD@{6}: initial pull

223  git init
225  git add src
229  git add project/Build.scala
234  git remote add origin git@github.com:Synesso/memx.git
250  git pull origin master

jem@jem-usb:~/projects$ mkdir x
jem@jem-usb:~/projects$ cd x
jem@jem-usb:~/projects/x$ git init
Initialized empty Git repository in /home/jem/projects/x/.git/
jem@jem-usb:~/projects/x$ echo "hi" > hello.world
jem@jem-usb:~/projects/x$ git add hello.world
jem@jem-usb:~/projects/x$ git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
#   (use "git rm --cached <file>..." to unstage)
#
#       new file:   hello.world
#
jem@jem-usb:~/projects/x$ ls -asl
total 24
 4 drwxrwxr-x 3 jem jem 4096 Apr 28 20:56 .
 4 drwxr-xr-x 8 jem jem 4096 Apr 28 20:56 ..
 4 drwxrwxr-x 7 jem jem 4096 Apr 28 20:56 .git
12 -rw-rw-r-- 1 jem jem    3 Apr 28 20:56 hello.world
jem@jem-usb:~/projects/x$ git remote add origin git@github.com:Synesso/memx.git
jem@jem-usb:~/projects/x$ git reflog
fatal: bad default revision 'HEAD'
jem@jem-usb:~/projects/x$ git pull origin master
remote: Counting objects: 7, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 7 (delta 0), reused 3 (delta 0)
Unpacking objects: 100% (7/7), done.
From github.com:Synesso/memx
 * branch            master     -> FETCH_HEAD
jem@jem-usb:~/projects/x$ ls -asl
total 36
 4 drwxrwxr-x 3 jem jem 4096 Apr 28 20:53 .
 4 drwxr-xr-x 8 jem jem 4096 Apr 28 20:52 ..
 4 drwxrwxr-x 8 jem jem 4096 Apr 28 20:53 .git
12 -rw-rw-r-- 1 jem jem   59 Apr 28 20:53 .gitignore
12 -rw-rw-r-- 1 jem jem    9 Apr 28 20:53 README.md
jem@jem-usb:~/projects/x$ git reflog
c80135d HEAD@{0}: initial pull

hostB$ cd /tmp; mkdir repo; cd repo; git init
Initialized empty Git repository in /tmp/repo/.git/
hostB$ : > .gitignore; echo this is a readme > README.md
hostB$ git add .; git commit -m initial
[master (root-commit) 58d43bd] initial
 1 files changed, 1 insertions(+), 0 deletions(-)
 create mode 100644 .gitignore
 create mode 100644 README.md

hostA$ cd /tmp; mkdir repo; cd repo; git init
Initialized empty Git repository in /tmp/repo/.git/
hostA$ echo hi > hello.world
hostA$ git add hello.world
hostA$ git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
#   (use "git rm --cached <file>..." to unstage)
#
#   new file:   hello.world
#
hostA$ git remote add origin ssh://hostB.dom.ain/tmp/repo
hostA$ git pull origin master
remote: Counting objects: 4, done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 4 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (4/4), done.
From ssh://hostB.dom.ain/tmp/repo
 * branch            master     -> FETCH_HEAD
hostA$ ls
README.md

hostA$ git fsck --lost-found
Checking object directories: 100% (256/256), done.
dangling blob 45b983be36b73c0788dc9cbcb76cbb80fc7bb057
hostA$

git init; echo "Readme" > Readme; git add Readme; git commit -m 'Initial commit'

git-pull.sh |    3 +++
 1 file changed, 3 insertions(+)

diff --git a/git-pull.sh b/git-pull.sh
index 2a10047..da102d0 100755
--- a/git-pull.sh
+++ b/git-pull.sh
@@ -261,6 +261,9 @@ esac

 if test -z "$orig_head"
 then
+       test $(git ls-files | wc -l) = 0 ||
+       die "$(gettext "Uncommitted changes in the index")"
+
       git update-ref -m "initial pull" HEAD $merge_head "$curr_head" &&
       git read-tree -m -u HEAD || exit 1
       exit