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On drush 4.5 with drush_make 6.x-2.x-dev works fine downloads modules and leaves modules already in sites/modules there.
Drush 5.1 with drush_make in core overrides the modules folder with the downloaded packages.
I figure the problem is the version of drush make add to 5.1 is the 6.x-2.3 and not the dev version.
Please can someone have a look.