Make sure ref to prune is in packed refs

Make sure ref to prune is in packed refs

RefDirectory:pack might raise an NPE when deleting loose
refs as final part of the RefDirectory.pack().

This is what the code does:
1) packed ref update: update the list of refs which will be
persisted in packed-refs
2) persit packed-refs: flush on file the refs computed in #1
3) prune loose refs: prune loose refs that have been packed in #2

The code correctly locks the packed-refs file during phases 1 to 3.
However, it makes the wrong assumption of considering
the loose refs set as immutable between phases 1 and 3.

The number and values of loose refs on the filesystem can mutate
at any time whilst the RefDirectory.pack() is in progress.
Assuming the contrary can lead to an NPE when retrieving refs
from the mutable loose refs list during phase #3.

Make sure that the ref is not null before dereferencing its
object-id value.

Bug: jgit-4
Change-Id: I2cd01f8a880f3c6561ad978a389ec2db45b6018b