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By committing Registry Rebuild into the distro (as per https://drupal.org/node/1983606#comment-7788313), any person who has Registry Rebuild installed the correct way (in their .drush folder) will receive errors about redeclaring registry_rebuild_* functions when running Drush, which for users installing a site into Commons via Aegir means that they can not install said site at all.
Work around is to have the user remove or move their local copy of Registry Rebuild, but it's not really a nice solution.
Patch coming to remove the entry from the makefile.