Files in a folder with a file that has no extension are not filtered

When using create-from-project, the filtering works but the filtered file is later overwritten with the original unfiltered content. The overwrite occurs due to an overly broad fileset (**/*) created due to the presence of a file with no extension in the folder.

We rely on the secondLevelResourceDirectory structure to include the directory.

Working on a PR.

Also broken in 3.2.1-SNAPSHOT

Example file structure that exhibits the bug:

• build
  • docker
    • Dockerfile
    • should-be-filtered-but-is-not.yaml