The goal is to externalize repositories declaration to a clean list of files managed inside the buildSrc directory.
By changing the gradlew, the starting experience is identical, and when using pure gradle adding "--init-script buildSrc/repo-init.gradle" will do the trick.
We are now using this layout for most of our project and it proved quite clean.
Furthermore it is possible to add:

apply from: buildSrc/repositories.gradle

in any gradle build file to have a clean import of the repositories declaration.

This might be solved by the Init script improvements in m7, since you can put repositories.gradle in .gradle/init.d/. Though I'm waiting for an equivalent of init.d for gradlew.

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Thanks again for reporting this issue. We haven't heard back from you after our inquiry from November 15th. We are closing this issue now. Please create an issue on GitHub if you still feel passionate about getting it resolved.