Git commit delete all files in repo

Question

The second time today git commit -m "don't quit me now"deletes all my repo. The way it is:

$ git add .
$ git commit -m "please, be gentle"

[master 7af0e9c] please, be gentle
140 files changed, 0 insertions(+), 3186 deletions(-)
delete mode 100644 .DS_Store
delete mode 100644 .gitignore
delete mode 100644 .rspec
delete mode 100644 Gemfile
...

I use Github for Mac along with the command line and wonder if this is so?

$ git checkout
$ git status
# On branch master
# Your branch is ahead of 'origin/master' by 1 commit.
#
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#   deleted:    .DS_Store
#   deleted:    .gitignore
#   deleted:    .rspec
#   deleted:    Gemfile
#   deleted:    Gemfile.lock

Answer 1

Since it git statustells you that everything is done for deletion, before doing anything else, reset the index HEAD:

git reset HEAD

After that git statusshould echo

no changes added to commit (use "git add" and/or "git commit -a")

Then try again:

git add .
git commit -m "new try"