Move all Drupal modules in sites/all/modules to sites/all/modules/contrib

gistfile1.sh

#!/bin/bash

# First install registry_rebuild : drush dl registry_rebuild
# Execute the following :
for dir in */; do dir=${dir%*/}; if [ "custom" != "${dir}" -a "contrib" != "${dir}" ]; then mv ${dir} contrib/${dir}; fi; done

# Run registry_rebuild and clear all caches : drush rr && drush cc all
# Fingers crossed...

# To update your git repo afterwards, just use : git add -u