build: Use nextflow gradle plugin

[edmundmiller]

This pull request refactors the build and plugin management system for the project, simplifying the Makefile, removing the root-level plugins/build.gradle, and updating Gradle settings for plugin management. The changes streamline how plugins are built, tested, installed, and released, and shift plugin configuration to a more modern Gradle setup.

Follows https://www.nextflow.io/docs/latest/guides/migrate-plugin.html

[pditommaso]

Worth to resume this now that the registry is avail