Add a few more places in "commit" and "checkout" that make sure
that the cache-tree is fully populated in the index.
* dt/cache-tree-repair:
cache-tree: do not try to use an invalidated subtree info to build a tree
cache-tree: Write updated cache-tree after commit
cache-tree: subdirectory tests
test-dump-cache-tree: invalid trees are not errors
cache-tree: create/update cache-tree on checkout