Merge branch 'dt/cache-tree-repair' into jch

Merge branch 'dt/cache-tree-repair' into jch

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: 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

# Conflicts:
# 	builtin/checkout.c
# 	builtin/commit.c