repair command: add handling of git-annex branch and index

Command/Repair.hs

@@ -10,7 +10,9 @@ module Command.Repair where
 import Common.Annex
 import Command
 import qualified Annex
-import Git.RecoverRepository (runRecovery)
+import qualified Git.Repair
+import qualified Annex.Branch
+import Git.Fsck (MissingObjects)
 
 def :: [Command]
 def = [noCommit $ dontCheck repoExists $
@@ -20,6 +22,37 @@ seek :: [CommandSeek]
 seek = [withNothing start]
 
 start :: CommandStart
-start = next $ next $ do
-	force <- Annex.getState Annex.force
-	inRepo $ runRecovery force
+start = next $ next $ runRepair =<< Annex.getState Annex.force
+
+runRepair :: Bool -> Annex Bool
+runRepair forced = do
+	(ok, stillmissing) <- inRepo $ Git.Repair.runRepair forced
+	when ok $
+		repairAnnexBranch stillmissing
+	return ok
+
+{- After git repository repair, the .git/annex/index file could
+ - still be broken, by pointing to bad objects, or might just be corrupt on
+ - its own. Since this index file is not used to stage things
+ - for long durations of time, it can safely be deleted if it is broken.
+ -
+ - Otherwise, commit the index file to the git-annex branch.
+ - This way, if the git-annex branch got rewound to an old version by
+ - the repository repair, or was completely deleted, this will get it back
+ - to a good state. Note that in the unlikely case where the git-annex
+ - branch is ok, and has new changes from elsewhere not yet reflected in
+ - the index, this does properly merge those into the index before
+ - committing.
+ -}
+repairAnnexBranch :: MissingObjects -> Annex ()
+repairAnnexBranch missing = ifM okindex
+	( do
+		Annex.Branch.forceCommit "committing index after git repository repair"
+		liftIO $ putStrLn "Successfully recovered the git-annex branch using .git/annex/index"
+	, do
+		inRepo $ nukeFile . gitAnnexIndex
+		liftIO $ putStrLn "Had to delete the .git/annex/index file as it was corrupt. It would be a very good idea to run: git annex fsck --fast"
+	)
+  where
+	okindex = Annex.Branch.withIndex $
+		inRepo $ Git.Repair.checkIndex missing