Fix some observed problems with incorrect diffs

This was never really working right because we were checking the
wrong flag and not checking it in all the places that we need to
be checking it.  I finally got around to writing a test and adding
actual support for it.

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.

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.

It seems that to implement these options, we just have to pass
the appropriate flags through to the libxdiff code taken from
core git.  So let's do it (and add a test).

Instead of having functions with so very many parameters to pass
hunk and line data, this takes the existing git_diff_hunk struct
and extends it with more hunk data, plus adds a git_diff_line.
Those structs are used to pass back hunk and line data instead of
the old APIs that took tons of parameters.

Some work that was previously only being done for git_diff_patch
creation (scanning the diff content for exact line counts) is now
done for all callbacks, but the performance difference should not
be noticable.

This lays groundwork for separating formatting options from diff
creation options.  This groups the formatting flags separately
from the diff list creation flags and reorders the options.  This
also tweaks some APIs to further separate code that uses patches
from code that just looks at git_diffs.