Add complex checkout test and then fix checkout

Add complex checkout test and then fix checkout

This started as a complex new test for checkout going through the
"typechanges" test repository, but that revealed numerous issues
with checkout, including:

* complete failure with submodules
* failure to create blobs with exec bits
* problems when replacing a tree with a blob because the tree
  "example/" sorts after the blob "example" so the delete was
  being processed after the single file blob was created

This fixes most of those problems and includes a number of other
minor changes that made it easier to do that, including improving
the TYPECHANGE support in diff/status, etc.