Update smudged entries when writing index

Overload DirCache.lock to take a repository that is
used for updating smudged index entries with information
from the repository's working tree.

New unit tests are also added for updating smudged index
entries on reset, checkout, and commit.

Change-Id: I88689f26000e4e57e77931e5ace7c804d92af1b6
5 files changed