COMMIT_EDITMSG not updated after pre-commit hook

["Hinrik Örn Sigurðsson" <hinrik.sig@gmail.com>]

I have a pre-commit hook which extracts documentation from file $foo
if it has pending changes to be committed. The hook creates/updates
the documentation file and calls "git add" on it.

When I do "git commit", the COMMIT_EDITMSG delivered to my editor
notes that this documentation file has been created/updated, but not
that its changes have been added to the index. However, if I go ahead
with the commit, I can see that the doc file changes were indeed
committed.

Here is a simplified test case:

$ cat .git/hooks/pre-commit
#!/usr/bin/env perl
use strict;
use warnings;

my $old = qx"git rev-parse HEAD:foo 2>/dev/null";
my $new = qx"git rev-parse :foo 2>/dev/null";

if (($? >> 8) != 0 || $old ne $new) {
    system "cat source > dest";
    system "git add dest";
}

$ ls
source

$ echo 123 >> source

$ git status
# On branch master
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#	modified:   source
#
no changes added to commit (use "git add" and/or "git commit -a")

$ git commit -a
Test commit
# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit.
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#       modified:   source
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       dest
[master 535ed7f] Test commit
 2 files changed, 3 insertions(+), 0 deletions(-)
 create mode 100644 dest

$ git status
# On branch master
nothing to commit (working directory clean)