The way eZ Publish 5 is built and shipped is a problem for projects authors/mainteners.

It forces you to modify existing directorie & files (config.yml, EzPublishKernel.php, ...) This is an issue for upgrades and for maintenance, since you need to manually maintain your files, maybe perform complex GIT manipulations.

This pull-request shows how it could be quite easy to make the default file some kind of "base" setup, that gets overridden by project files, but without touching them: https://github.com/ezsystems/ezpublish-community/pull/97.