Add excluded dependencies to the shadow configuration automatically

In my project I have to relocate a dependency because it clashes with a different version of the same dependency in the environment where my project is used. So I do:

dependencies {
    compile 'org.metaborg:org.metaborg.core:2.1.0-SNAPSHOT'
    compile 'commons-io:commons-io:2.4'
}

shadowJar {
    relocate 'org.apache.commons.io', 'shadow.org.apache.commons.io'
}

Now, because I relocated the dependency, I have to include in my shadowed jar all dependencies that themselves depend on the relocated dependency. But these dependencies transitively depend on other dependencies that I would like to exclude from the Jar. They should just be normal dependencies.

shadowJar {
    relocate 'org.apache.commons.io', 'shadow.org.apache.commons.io'

    dependencies {
        include(dependency('org.metaborg::'))
        include(dependency('commons-io:commons-io'))
   }
}

Doing this, I would expect the excluded (transitive) dependencies to be added to the shadow configuration automatically, since they are still dependencies my project or the shadowed jars. This appears not to be the case, and I would have to manually add all transitive dependencies to the shadow configuration. This is error prone, and as soon as one of my dependencies changes its own dependencies, I'd have to change my script.

Is there a way to add dependencies not included in the uber jar automatically to the shadow configuration?

Start by tracing the shadowJar dependencies block and how excluded transitive dependencies are handled in the shadow configuration. Done means dependencies omitted from the uber JAR are added to the shadow configuration automatically without manually listing every transitive dependency; the issue names no files or tests to run.