_loader/loadelement.py: Use enumerate() in dependency extraction

In cases where elements end up with large numbers of dependencies,
the n-squared performance in `_extract_depends_from_node` can produce
significant delays during project load.  This patch corrects that.
In addition we were double-retrieving provenance which was unnecessary.

Signed-off-by: Daniel Silverstone <daniel.silverstone@codethink.co.uk>