Do not extract Metadata for missing unmanaged files

[thardeck]

Make sure that files exist before extracting the metadata and remove them from the unmanaged-files list if not.

This should allow filtering to work properly because the filters are applied before extraction so it is possible for the user to filter directories with changing files. Before that machinery-helper could crash if a file was removed during the first phase of inspection and there was no way for the user to filter these directories because the helper does not support filtering yet.

[thardeck]

To test it you can run the following command inside a managed repository:

for i in `seq 1 600`; do touch "$i"; sleep 1; rm "$i"; done

[manno]

LGTM