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This is still reproducible in recent Gradle.

I am not quite sure why you used fileTree for iterating over the runtime dependencies. Either way, the following works in both cases:

task printDeps << {
    println "Printing ${name} dependencies:"
    configurations.runtime.each {
        println it
    }
}

Well, I can ask you why I should not!

Anyway, a long time has passed and this was just a sample to reproduce the problem. What I think I was trying to achieve was to copy all the JARs a project depended on to a target folder.
After all, if a configuration has a "asFileTree" method, I think it should work as expected or at least it should be well documented. Please note I don't have current Javadoc/Groovydoc with me to check what the documentation says.

If you ask for the FileTree then you are only getting the root folder but not the actual files. You'd either have to call the method getFiles() to get the flattened list or iterate over the files with the method visit. I think the documentation is fairly clear about though I can see how you could miss those details.

I am of course iterating over the files (see the sample project), the problem is that the B.jar is not among the dependency files if B has not yet been built, like if it were not a dependency.