Only the staged file is committed.

$ git commit -m "first version of config.pl"
[master cdd2c3b] first version of config.pl
 1 file changed, 1 insertion(+)
 create mode 100644 config.pl
$ git status
examples/out/status_08.txt
# On branch master
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#       modified:   README.txt
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       setup.pl
no changes added to commit (use "git add" and/or "git commit -a")