better handling of missing index file

Assistant/Threads/SanityChecker.hs

@@ -40,13 +40,18 @@ sanityCheckerStartupThread startupdelay = namedThreadUnchecked "SanityCheckerSta
 
 	{- A corrupt index file can prevent the assistant from working at
 	 - all, so detect and repair. -}
-	unlessM (liftAnnex $ inRepo $ checkIndex S.empty) $ do
+	ifM (liftAnnex $ inRepo $ checkIndex S.empty)
-		debug ["corrupt index found at startup; removing"]
+		( do
-		liftAnnex $ inRepo nukeIndex
+			debug ["corrupt index file found at startup; removing and restaging"]
-		{- Normally the startup scan avoids re-staging files,
+			liftAnnex $ inRepo nukeIndex
-		 - but with the index deleted, everything needs to be
+			{- Normally the startup scan avoids re-staging files,
-		 - restaged. -}
+			 - but with the index deleted, everything needs to be
-		modifyDaemonStatus_ $ \s -> s { forceRestage = True }
+			 - restaged. -}
+			modifyDaemonStatus_ $ \s -> s { forceRestage = True }
+		, whenM (liftAnnex $ inRepo missingIndex) $ do
+			debug ["no index file; restaging"]
+			modifyDaemonStatus_ $ \s -> s { forceRestage = True }
+		)
 
 	{- If there's a startup delay, it's done here. -}
 	liftIO $ maybe noop (threadDelaySeconds . Seconds . fromIntegral . durationSeconds) startupdelay

Git/Repair.hs

@@ -13,6 +13,7 @@ module Git.Repair (
 	resetLocalBranches,
 	removeTrackingBranches,
 	checkIndex,
+	missingIndex,
 	nukeIndex,
 	emptyGoodCommits,
 ) where
@@ -369,18 +370,19 @@ verifyTree missing treesha r
 			else cleanup
 
 {- Checks that the index file only refers to objects that are not missing,
- - and is not itself corrupt or missing. -}
+ - and is not itself corrupt. Note that a missing index file is not
+ - considered a problem (repo may be new). -}
 checkIndex :: MissingObjects -> Repo -> IO Bool
-checkIndex missing r = ifM (doesFileExist (localGitDir r </> "index"))
+checkIndex missing r = do
-	( do
+	(bad, _good, cleanup) <- partitionIndex missing r
-		(bad, _good, cleanup) <- partitionIndex missing r
+	if null bad
-		if null bad
+		then cleanup
-			then cleanup
+		else do
-			else do
+			void cleanup
-				void cleanup
+			return False
-				return False
+
-	, return False
+missingIndex :: Repo -> IO Bool
-	)
+missingIndex r = not <$> doesFileExist (localGitDir r </> "index")
 
 partitionIndex :: MissingObjects -> Repo -> IO ([LsFiles.StagedDetails], [LsFiles.StagedDetails], IO Bool)
 partitionIndex missing r = do