Further threading fixes

Further threading fixes

This builds on the earlier thread safety work to make it so that
setting the odb, index, refdb, or config for a repository is done
in a threadsafe manner with minimized locking time.  This is done
by adding a lock to the repository object and using it to guard
the assignment of the above listed pointers.  The lock is only
held to assign the pointer value.

This also contains some minor fixes to the other work with pack
files to reduce the time that locks are being held to and fix an
apparently memory leak.