The repair code assumed that if fsck found no broken objects, after
removing bad objects and possibly pulling replacements from remote, all was
well.. but this is not really true. Removing bad objects could leave some
branches broken. fsck doesn't report any missing objects in this case,
and its messages about broken branches are ignored by the fsck output
parser.
To deal with this, added a separate scan of all refs to find broken ones
and remove them when --forced. This will also let anyone who ran into this
bug run repair again to fix up the incomplete repair done before.
This commit was sponsored by Aaron Whitehouse.
Removed instance, got it all to build using fromRef. (With a few things
that really need to show something using a ref for debugging stubbed out.)
Then added back Read instance, and made Logs.View use it for serialization.
This changes the view log format.
Fixes a test case I received where a corrupted repo was repaired, but the
git-annex branch was not. The root of the problem was that the
MissingObject returned by the repair code was not necessarily a complete
set of all objects that might have been deleted during the repair.
So, stop trying to return that at all, and instead make the index file
checking code explicitly verify that each object the index uses is present.
