When determining diffs between two iterators we may need to
recurse into an unmatched directory for the "new" iterator when
it is either a prefix to the current item of the "old" iterator
or when untracked/ignored changes are requested by the user and
the directory is untracked/ignored.

When advancing into the directory and no files are found, we will
get back `GIT_ENOTFOUND`. If so, we simply skip the directory,
handling resulting unmatched old items in the next iteration. The
other case of `iterator_advance_into` returning either
`GIT_NOERROR` or any other error but `GIT_ENOTFOUND` will be
handled by the caller, which will now either compare the first
directory entry of the "new" iterator in case of `GIT_ENOERROR`
or abort on other cases.

Improve readability of the code to make the above logic more
clear.

Remove some unused functions, refactor some ugliness.

When a directory is removed out from underneath us, stop trying to
manipulate it.

Drop some of the layers of indirection between the workdir and the
filesystem iterators.  This makes the code a little bit easier to
follow, and reduces the number of unnecessary allocations a bit as
well.  (Prior to this, when we filter entries, we would allocate them,
filter them and then free them; now we do the filtering before
allocation.)

Also, rename `git_iterator_advance_over_with_status` to just
`git_iterator_advance_over`.  Mostly because it's a fucking long-ass
function name otherwise.

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