Fix issue where bake was missing habtm associations

If the current model is not the first table, habtm associations would be
missed. This was caused by eff4004261a2bd05e4df54ee2af057c680ff50fc

Refs #3532
Fixes #3605
app\ \skel\ sync, copyright update, gitignore

Brought \app\ and \lib\Cake\Console\Templates\skel\ in sync

Fixed various @package annotations in \app\

Re-renamed .gitignore

Fixed various @package annotations in \lib\Cake\Console\Templates\skel\

Changed .gitignore to only ignore /app/Config/database.php instead of all files in /app/Config/ (helps to keep it in sync with its skel folder!)

Added some good practice rules from https://help.github.com/articles/ignoring-files to gitignore

Brought previously forgotten/not committed files in sync (again)

Updated all copyrights to 2013 (I think I found all, even some outdated)

Added previously unversioned file which was created during sync of \app\ and \lib\Cake\Console\Templates\skel\