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.
Report the index being locked with its own error code in order to be
able to differentiate, as a locked index is typically the result of a
crashed process or concurrent access, both of which often require user
intervention to fix.
This fixes some places where the new tests were leaving the test
area in a bad state or were freeing data they should not free.
It also removes code that is extraneous to the core issue and
fixes an invalid SHA being looked up in one of the tests (which
was failing, but for the wrong reason).
