Delete any unused Drupal module directories. Assumes '/sites/all/modules/contrib' etc. directory structure, hence depth of 5. Change this if required. Removes any directories that contain no enabled modules, taking into account sub-modules.

gistfile1.txt

drush sqlq "SELECT DISTINCT SUBSTRING_INDEX(filename , '/', 5) dir
FROM system
WHERE status = 0
AND type = 'module'
AND filename NOT LIKE 'modules/%'
HAVING dir NOT IN (
  SELECT SUBSTRING_INDEX(filename , '/', 5)
  FROM system
  WHERE status = 1
);" | xargs rm -rf