drush cannot redeclare : it loads duplicate command files

Looks like #644126: drush loads duplicate command files which has been fixed some time ago.

With Drush 5.10.0.

Modules should be able to be duplicated in /profiles/ and /sites/all/modules/ as in /sites/example.org/modules/. And drush should take care of that.

Impact:

• Some sites, at least Openatrium ones ("sites/all/modules" vs "profiles/openatrium/modules"), cannot migrate between platforms.
• Importing sites into aegir fails if they contain one or more duplicated modules between the platform (sites/all/modules) and their site's directory (sites/example.org/modules).
• Maybe some migrations and backups with Provision CiviCRM.

Example:

Drush command terminated abnormally due to an unrecoverable error. Error: Cannot redeclare l10n_update_drush_command() (previously declared in /srv/aegir/platforms/drupal-6-2013.11.21-prod/sites/all/modules/contrib/l10n_update/l10n_update.drush.inc:12) in /srv/aegir/platforms/drupal-6-2013.11.21-prod/profiles/openatrium/modules/l10n/l10n_update/l10n_update.drush.inc, line 30

Internal reference numbers:

• redmine 12563 (openatrium migration)
• redmine 13143 (openatrium migration)
• redmine 13206 (backup in aegir with provision_civicrm)

Upstream:

• https://github.com/drush-ops/drush/issues/280 has a working patch for 5.10 and a pull request
• http://drupal.stackexchange.com/questions/83959/cannot-redeclare-librari... answered but not fixed