I tried to fix the concrete case by changing the input of the task in question. But the Android Gradle Plugin hard codes things so much that it is not possible to remove/change what it does when setting up the LinkTask. This is too opinionated in my mind. The nice thing about Gradle is usually that even if there are shortcoming like this, you can still do some customisation by reconfiguring tasks directly. It's unfortunate, that the Android Plugin seems to remove this flexibility on purpose (e.g. by calling

disallowChanges()

on task input file collections).

Funny enough, this highlights how good it would be if more libraries/tools would detect such issues in their own builds already before they publish their dependencies. Problem is caused because

com.android.tools:repository

directly depends on the

javax

while it's transitive dependency depends on the same under the

jakarta

name. I doubt that this mismatch is on purpose.

FTR: Best solution I could come up with was to fix the metadata of

com.android.tools:repository

so that the conflict would not arise in the first place:

withModule("com.android.tools:repository") {
        allVariants {
            withDependencies {
                removeIf { it.name == "javax.activation" }
                add("jakarta.activation:jakarta.activation-api")
            }
        }
    }

And this all on top that there are already conflicts, because often there is an API

jar

and an implementation

jar

, where the implementation also includes the API classes.

And then there are copies of some of the APIs under different names by glassfish and tomcat etc. So even without the name change the situation was already (too) complex.