Remove usage of deprecated API:
  - ModuleFileSystem -> FileSystem
  - File#fromIOFile(...) -> File#create(relativPath): remove usage of ProjectFileSystem in unit tests.
Remove AbstractSourceImporter depracted extension point: PHPSourceImporter.
Remove usage of deprecated API:
      - ModuleFileSystem -> FileSystem
      - File#fromIOFile(...) -> File#create(relativPath): remove usage of ProjectFileSystem in unit tests.