Ensure that `git_index_read_index` clears the uptodate bit on
files that it modifies.
Further, do not propagate the cache from an on-disk index into
another on-disk index. Although this should not be done, as
`git_index_read_index` is used to bring an in-memory index into
another index (that may or may not be on-disk), ensure that we do
not accidentally bring in these bits when misused.
Test that entries are only smudged when we write the index: the
entry smudging is to prevent us from updating an index in a way
that it would be impossible to tell that an item was racy.
Consider when we load an index: any entries that have the same
(or newer) timestamp than the index itself are considered racy,
and are subject to further scrutiny.
If we *save* that index with the same entries that we loaded,
then the index would now have a newer timestamp than the entries,
and they would no longer be given that additional scrutiny, failing
our racy detection! So test that we smudge those entries only on
writing the new index, but that we can detect them (in diff) without
having to write.
Keep track of entries that we believe are up-to-date, because we
added the index entries since the index was loaded. This prevents
us from unnecessarily examining files that we wrote during the
cleanup of racy entries (when we smudge racily clean files that have
a timestamp newer than or equal to the index's timestamp when we
read it). Without keeping track of this, we would examine every
file that we just checked out for raciness, since all their timestamps
would be newer than the index's timestamp.
