Improve repair of git-annex index file.

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.

Command/Repair.hs

@@ -12,7 +12,6 @@ import Command
 import qualified Annex
 import qualified Git.Repair
 import qualified Annex.Branch
-import Git.Fsck (MissingObjects)
 import Git.Types
 import Annex.Version
 
@@ -28,12 +27,12 @@ start = next $ next $ runRepair =<< Annex.getState Annex.force
 
 runRepair :: Bool -> Annex Bool
 runRepair forced = do
-	(ok, stillmissing, modifiedbranches) <- inRepo $
+	(ok, modifiedbranches) <- inRepo $
 		Git.Repair.runRepair forced
 	-- This command can be run in git repos not using git-annex,
 	-- so avoid git annex branch stuff in that case.
 	whenM (isJust <$> getVersion) $
-		repairAnnexBranch stillmissing modifiedbranches
+		repairAnnexBranch modifiedbranches
 	return ok
 
 {- After git repository repair, the .git/annex/index file could
@@ -50,8 +49,8 @@ runRepair forced = do
  - yet reflected in the index, this does properly merge those into the
  - index before committing.
  -}
-repairAnnexBranch :: MissingObjects -> [Branch] -> Annex ()
-repairAnnexBranch missing modifiedbranches
+repairAnnexBranch :: [Branch] -> Annex ()
+repairAnnexBranch modifiedbranches
 	| Annex.Branch.fullname `elem` modifiedbranches = ifM okindex
 		( commitindex
 		, do
@@ -63,8 +62,7 @@ repairAnnexBranch missing modifiedbranches
 		, nukeindex
 		)
   where
-	okindex = Annex.Branch.withIndex $
-		inRepo $ Git.Repair.checkIndex missing
+	okindex = Annex.Branch.withIndex $ inRepo $ Git.Repair.checkIndex
 	commitindex = do
 		Annex.Branch.forceCommit "committing index after git repository repair"
 		liftIO $ putStrLn "Successfully recovered the git-annex branch using .git/annex/index"