That is why maven offers a plugin model for your custom logic that can be written in Java/Kotlin and a well defined lifecycle model where you can configure your plugin declaratively.
You can also download custom CLI tools and invoke them as part of a well-defined build lifecycle.
And then fail to do proper incremental builds, leaving you with no choice but a faulty build or clean installing on every occasion.
At the very least, I would move to Gradle which does have proper knowledge of your build graph. But Mill is also a good choice and fills the same niche, with the added benefit that imperative-looking ordinary scala code will simply become a parallelizable, cacheable build graph.
You can also download custom CLI tools and invoke them as part of a well-defined build lifecycle.