docker: skip unparseable YAML files across directories

Allow malformed YAML files to produce warnings and empty dependency results so multi-directory jobs can continue processing later valid directories.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Copilot-Session: 8546112f-5fd5-438e-92d2-7e66e51835ac