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.