Fix destination project might not be included

[SimonMarquis]

When filtering out projects with ProjectGenerator.includeProject, the process will throw a NoSuchElementException("Collection contains no element matching the predicate.") because the destination project has been filtered out of the root nodes.

I'm making it as a draft because I'd like to create a test for it (there might be the same issue as well for the DependencyGraphGenerator). The regression was introduced in https://github.com/vanniktech/gradle-dependency-graph-generator-plugin/commit/8f7c8296b704d84dde35a0d92b22f4b5d66a5a9b.