This script will
- fetch the latest changes from the git repo
- update the git submodules
- disable those modules listed in modules.disabled (and modules.mysite.disabled)
- enable those modules listed in modules.enabled (and modules.mysite.enabled)
- run the drupal module updates
Save the 2 scripts into the scripts dir of your project and chmod 0755 the file to make it executable. Then you just call "./scripts/local_update.sh mysite" where mysite is the instance name as the argument (so that it knows what modules.xxx.enabled/disabled to use). If you don't want to update your code you can also just call "./scripts/module.sh mysite" to just do the enabling/disabling of the modules.
These files contain the list of enabled and disabled modules. Just put the modules names, one per line. If you have subsites and you want to enable/disable specific modules for these sites, just create modules.mysite.enabled and modules.mysite.disabled files.
Make sure you have drush installed with version >= 3.0