Avoid duplicate sources, even if sourceSet directories overlap

[sambsnyd]

While not the default or a good idea, it is not impossible to have overlapping source directories. Example of such a configuration:

sourceSets {
  main {
    java.srcDirs = []
    groovy.srcDirs = ["src"]
    resources.srcDirs = ["src"]
  }
  ...
}

We should use our existing tracking of files which have already been parsed to exclude any duplicate source files from making their way into the final results.

[timtebeek]

Picked up in https://github.com/openrewrite/rewrite-gradle-plugin/commit/8c1986ca5420ad81a5eb7785240605db08d35cdc