Fix some of the glaring errors in GIT_DIFF_REVERSE

These changes fix the basic problem with GIT_DIFF_REVERSE being
broken for text diffs.  The reversed diff entries were getting
added to the git_diff correctly, but some of the metadata was kept
incorrectly in a way that prevented the text diffs from being
generated correctly.  Once I fixed that, it became clear that it
was not possible to merge reversed diffs correctly.  This has a
first pass at fixing that problem.  We probably need more tests
to make sure that is really fixed thoroughly.
Make diff and status perform soft index reload

This changes `git_index_read` to have two modes - a hard index
reload that always resets the index to match the on-disk data
(which was the old behavior) and a soft index reload that uses
the timestamp / file size information and only replaces the index
data if the file on disk has been modified.

This then updates the git_status code to do a soft reload unless
the new GIT_STATUS_OPT_NO_REFRESH flag is passed in.

This also changes the behavior of the git_diff functions that use
the index so that when an index is not explicitly passed in (i.e.
when the functions call git_repository_index for you), they will
also do a soft reload for you.

This intentionally breaks the file signature of git_index_read
because there has been some confusion about the behavior previously
and it seems like all existing uses of the API should probably be
examined to select the desired behavior.
Convert git_index_read to have a "force" flag

This is a little more intuitive than the turned-around option that
I originally wrote.
Add git_diff_options_init helper

Sometimes the static initializer for git_diff_options cannot be
used and since setting them to all zeroes doesn't actually work
quite right, this adds a new helper for that situation.

This also adds an explicit new value to the submodule settings
options to be used when those enums need static initialization.
More tests and fixed for merging reversed diffs

There were a lot more cases to deal with to make sure that our
merged (i.e. workdir-to-tree-to-index) diffs were matching the
output of core Git.