When diffing the index with the workdir and GIT_DIFF_UPDATE_INDEX has been passed,
the previous implementation was always writing the index to disk even if it wasn't
modified.

Fixed GIT_DELTA_CONFLICTED not returned in some cases

If an index entry for a file that is not in HEAD is in conflicted state,
when diffing HEAD with the index, the status field of the corresponding git_diff_delta was incorrectly reported as GIT_DELTA_ADDED instead of GIT_DELTA_CONFLICTED.

This was due to handle_unmatched_new_item() initially setting the status
to GIT_DELTA_CONFLICTED but then overriding it later with GIT_DELTA_ADDED.

When a file on the workdir has the same or a newer timestamp than the
index, we need to perform a full check of the contents, as the update of
the file may have happened just after we wrote the index.

The iterator changes are such that we can reach inside the workdir
iterator from the diff, though it may be better to have an accessor
instead of moving these structs into the header.

When updating the index during a diff, preserve the original mode,
which prevents us from dropping the mode to what we have interpreted
as on our system (eg, what the working directory claims it to be,
which may be a lie on some systems.)

Mark the `old_file` and `new_file` sides of a delta with a new bit,
`GIT_DIFF_FLAG_EXISTS`, that introduces that a particular side of
the delta exists in the diff.

This is useful for indicating whether a working directory item exists
or not, in the presence of a conflict.  Diff users may have previously
used DELETED to determine this information.

It's not always obvious the mapping between stage level and
conflict-ness.  More importantly, this can lead otherwise sane
people to write constructs like `if (!git_index_entry_stage(entry))`,
which (while technically correct) is unreadable.

Provide a nice method to help avoid such messy thinking.

Since a diff entry only concerns a single entry, zero the information
for the index side of a conflict.  (The index entry would otherwise
erroneously include the lowest-stage index entry - generally the
ancestor of a conflict.)

Test that during status, the index side of the conflict is empty.