Change preserve-paths to use "sites/all" to protect multisite folders. #472
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In the drupal 7 composer template, running composer install the first time (or when you delete vender folder) will silently remove any sites/X folders. This will destroy any multisites installed, and prevents the codebase from being used with systems like @aegirproject.
Changing the preserve-paths value to "web/sites" worked great for me.