I have discovered an issue in the gradle 2.5 and 2.6-RC2 with multi-project builds. Or perhaps is a feature. 
Anyway, what works with gradle 2.3 and 2.4 does not work anymore with gradle 2.5+.
I have created a small project that can reproduce the issue. It consists of a root project with two-subprojects
root_project
-> core
-> petshop
settings.gradle
The root project has only the settings.gradle file:
include "core"
include "petshop"
The core project has the following build.gradle:
apply plugin: 'java'
configurations{
cats
}
sourceSets {
cats
}
dependencies {
catsCompile project(':core')
}
jar {
archiveName = "animals.jar"
}
task createCats(type: Jar) {
from sourceSets.cats.output
archiveName "cats.jar"
}
artifacts {
cats createCats
}
The core sub-project produces two artifacts: the default animals.jar and the cats.jar from the cats configuration.
The petshop project build.gradle:
apply plugin: 'java'
dependencies {
compile project(':core') // required animals.jar
compile project(path: ':core', configuration: 'cats') // required cats.jar
}
jar {
archiveName = "petshop.jar"
}
The petshop project requires for compilation both animals.jar and cats.jar. But it seems that gradle places just one of the dependencies in the class-path of the petshop project. Depending of the order of the dependencies, the build fails finding classes from the animal.jar or cats.jar.
I have attached the project here, as I could not upload it.
https://drive.google.com/open?id=0B1tz713sef-Ta1VtWnRteVV4RFU