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I use drush make with a stub .make file to download a custom profile via git.

that profile has all of the modules I want all of my sites to start out with.

If I then go into that site, and run "drush up drupal", it will update core, and remove my custom profile.

This is not good, since all of the modules I downloaded with my install profile's make file get stuck into the profiles/myprofile/modules folder. This basically removes all of my installed contrib modules, and drush doesn't give me a way to put them any where else, so basically, I can't update core with drush.

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You should post a bug report about this in the Drush issue queue. (drupal.org/project/issues/drush) – greg_1_anderson Nov 15 '12 at 2:27
I did, though I was hesitant prior to posting here because I'm not entirely sure this isn't the intended behavior and I just don't understand it correctly. drupal.org/node/1841676 – CCMonkey Nov 15 '12 at 15:12

Consider to use Aegir. It supports this usecase.

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You should consider expanding this post, and explaining how exactly Aegir might help in this case. – AjitS Nov 22 '12 at 13:22

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