Fix TreeWalk to correctly handle missing subtrees

Fix TreeWalk to correctly handle missing subtrees

When we are walking through a pair of trees and one of the two trees has
added a new subtree in the middle we need to make sure we use the special
EmptyTreeIterator as a placeholder for the other tree which is missing
that path entry.

This fixes the issue Robin noticed where pulling up the difference for
"55e9a699df...5b07a80cf org.spearce.jgit.test" showed files deleted
by 5b07 when they were not even touched.  The addition of a new subtree
("revwalk") by 5b07 is what threw the iteration off, causing the other
tree (55e9's) to enter into the wrong subtree at the wrong time.

Signed-off-by: Shawn O. Pearce <spearce@spearce.org>
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>