What I think is an error can be nicely reproduced via the sample ear/earWithWar.
This project contains two subprojects: One that builds a war and another one that builds an ear which uses the war in a deploy dependency:
deploy project(':war')
I would expect that I’d find a war.war in the ear after gradle ear, but instead I see a war.jar.
Tested with gradle 2.4.
Instead I have to add the dependency like this:
deploy project(path: ':war', configuration: 'archives')
I’m ok with this but it would be good to document this.