When formatting a patch as email we do not include the commit's
message in the formatted patch output. Implement this and add a
test that verifies behavior.

When examining the working directory and determining whether it's
up-to-date, only consider the nanoseconds in the index entry when
built with `GIT_USE_NSEC`.  This prevents us from believing that
the working directory is always dirty when the index was originally
written with a git client that uinderstands nsecs (like git 2.x).

git_index_entry__init_from_stat: set nsec fields in entry stats

Although our index contains the literal time present in the index,
we do not read nanoseconds from disk, and thus we should not use
them in any comparisons, lest we always think our working directory
is dirty.

Guard this behind a `GIT_USE_NSECS` for future improvement.

When we're not doing pathspec matching, we let the iterator handle
file matching for us.  However, we can only trust the iterator to
return *files* that match the pattern, because the iterator must
return directories that are not strictly in the pathlist, but that
are the parents of files that match the pattern, so that diff can
later recurse into them.

Thus, diff must examine non-files explicitly before including them
in the delta list.