How to resolve circular dependencies between libraries at linking with GCC-Toolchain (building native binaries)?

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You can modify the list of arguments in withArguments any way you like, not just appending to the end.

linker.withArguments { args ->
    List origArgs = new ArrayList(args)
    args.clear()
    // do magic to recalcuate the argument list
    List newArgs = ["test"]
    args.addAll(newArgs)
}

I think this is going to make your build pretty fragile/sensitive to the argument ordering that Gradle produces. I think it would be better if you could avoid circular dependencies (maybe by sub-dividing your library more?).