Moved all packages into a new packages directory and added an __init__.py for the package_checker.

Updated .gitignore to ignore new batch/shell files.

Updated plugin_helpers/hooks.sh to link the operating system specific files on 'git pull' and 'git checkout'.

Updated config.sh to link the git hooks and force 'git checkout' to execute the hook.
Changed config.sh to setup.sh to match the batch naming.