I'll add this to VFSDeploymentUnit:

  |    /**
  |     * Gets the metadata files for this deployment unit
  |     * 
  |     * @param filter the file filter
  |     * @return the virtual files that match
  |     * @throws IllegalArgumentException if both the name and suffix are null
  |     */
  |    List<VirtualFile> getMetaDataFiles(VirtualFileFilter filter);
  | 

This will enable you to easily get what you're looking for.
e.g. if filter is instance of VirtualFileFilterWithAttributes it will also 
recurse into metadata locations

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