Every time I make significant changes to a Drupal module (i.e. new items in menu hook or changes to theme hook) I must go to admin/build/modules and click save again otherwise I cannot access the modifications I made.
Do you know if there is a better way to do that?
Thanks!
I would suggest drush and devel + admin which provides a much quicker way to doing mundane tasks like clearing cache.
These tools can save you countless hours when developing, once you learn how to use them. Drush is very capable and also provides shortcuts to installing modules and much more.