Make the `applyCwd()` methods handle `null` inputs
Make `pathsToFileList()` and `filesToPathList()` accept a simple `Collection` instead of a `List`
Make the `SourceArgumentsResolver` accept `null` for resoruces dirs to indicate we're not interested in resources
Changed `getCompilerOutDir()` to `getCompilerOutputRepo()` because it doesn't ahve to be a directory