conflict in /app/vendor

Perhaps this is compatibility issue with "https://github.com/dokku-alt/dokku-alt" , but I have conflict with 
/app/vendor.

Normally it contains some resources for nginx / php, however composer-php thinks he can simply clean it all out.

As this works on Heiroku , could you advise how is it configured exactly and I should be able to fix it for dokku-alt as well. 
