Revert "avoid double work in git-annex init"

This reverts commit 0f10f208a7.

The implementation of this turns out to be unsafe; it can lead to a keys
db deadlock. scanAnnexedFiles injects a call to inAnnex into
reconcileStaged, but inAnnex sometimes needs to read from the keys db,
which will try to re-open it when it's in the process of being opened.
The exclusive lock of gitAnnexKeysDbLock will then deadlock.

This needs to be done in some other way...

Annex/WorkTree.hs

@@ -69,30 +69,28 @@ ifAnnexed :: RawFilePath -> (Key -> Annex a) -> Annex a -> Annex a
 ifAnnexed file yes no = maybe no yes =<< lookupKey file
 
 {- Find all annexed files and update the keys database for them.
+ - 
+ - This is expensive, and so normally the associated files are updated
+ - incrementally when changes are noticed. So, this only needs to be done
+ - when initializing/upgrading a repository.
  -
  - Also, the content for an unlocked file may already be present as
  - an annex object. If so, populate the pointer file with it.
  - But if worktree file does not have a pointer file's content, it is left
  - as-is.
- -
- - Normally the keys database is updated incrementally when changes are
- - noticed. For an initial scan, this is faster than that incremental
- - update.
  -}
 scanAnnexedFiles :: Annex ()
-scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $
+scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ do
-	Database.Keys.runWriter' (Just reconciler) (const noop)
-  where
-	reconciler dbh = do
 	g <- Annex.gitRepo
-		liftIO $ Database.Keys.SQL.dropAllAssociatedFiles dbh
+	Database.Keys.runWriter $
+		liftIO . Database.Keys.SQL.dropAllAssociatedFiles
 	(l, cleanup) <- inRepo $ Git.LsTree.lsTree
 		Git.LsTree.LsTreeRecursive
 		(Git.LsTree.LsTreeLong True)
 		Git.Ref.headRef
-		catObjectStreamLsTree l want g (go dbh)
+	catObjectStreamLsTree l want g go
 	liftIO $ void cleanup
-	
+  where
 	-- Want to process symlinks, and regular files.
 	want i = case Git.Types.toTreeItemType (Git.LsTree.mode i) of
 		Just Git.Types.TreeSymlink -> Just (i, False)
@@ -105,16 +103,17 @@ scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $
 		Just n | n < maxPointerSz -> Just (i, True)
 		_ -> Nothing
 	
-	go dbh getnext = liftIO getnext >>= \case
+	go getnext = liftIO getnext >>= \case
 		Just ((i, isregfile), Just c) -> do
-			maybe noop (add i isregfile dbh)
+			maybe noop (add i isregfile)
 				(parseLinkTargetOrPointer (L.toStrict c))
-			go dbh getnext
+			go getnext
 		_ -> return ()
 	
-	add i isregfile dbh k = do
+	add i isregfile k = do
 		let tf = Git.LsTree.file i
-		liftIO $ Database.Keys.SQL.addAssociatedFileFast k tf dbh
+		Database.Keys.runWriter $
+			liftIO . Database.Keys.SQL.addAssociatedFileFast k tf
 		whenM (pure isregfile <&&> inAnnex k) $ do
 			f <- fromRepo $ fromTopFilePath tf
 			liftIO (isPointerFile f) >>= \case

Database/Keys.hs

@@ -23,7 +23,6 @@ module Database.Keys (
 	removeInodeCache,
 	isInodeKnown,
 	runWriter,
-	runWriter',
 ) where
 
 import qualified Database.Keys.SQL as SQL
@@ -74,7 +73,7 @@ runReader a = do
 		v <- a (SQL.ReadHandle qh)
 		return (v, st)
 	go DbClosed = do
-		st' <- openDb True Nothing DbClosed
+		st' <- openDb True DbClosed
 		v <- case st' of
 			(DbOpen qh) -> a (SQL.ReadHandle qh)
 			_ -> return mempty
@@ -88,15 +87,7 @@ runReaderIO a = runReader (liftIO . a)
  -
  - The database is created if it doesn't exist yet. -}
 runWriter :: (SQL.WriteHandle -> Annex ()) -> Annex ()
-runWriter = runWriter' Nothing
+runWriter a = do
-
-runWriterIO :: (SQL.WriteHandle -> IO ()) -> Annex ()
-runWriterIO a = runWriter (liftIO . a)
-
-{- When a reconcile action is passed, it is run by reconcileStaged instead
- - of its usual scan, and must update the database in the same way. -}
-runWriter' :: Maybe (SQL.WriteHandle -> Annex ()) -> (SQL.WriteHandle -> Annex ()) -> Annex ()
-runWriter' reconciler a = do
 	h <- Annex.getRead Annex.keysdbhandle
 	withDbState h go
   where
@@ -104,12 +95,15 @@ runWriter' reconciler a = do
 		v <- a (SQL.WriteHandle qh)
 		return (v, st)
 	go st = do
-		st' <- openDb False reconciler st
+		st' <- openDb False st
 		v <- case st' of
 			DbOpen qh -> a (SQL.WriteHandle qh)
 			_ -> error "internal"
 		return (v, st')
 
+runWriterIO :: (SQL.WriteHandle -> IO ()) -> Annex ()
+runWriterIO a = runWriter (liftIO . a)
+
 {- Opens the database, creating it if it doesn't exist yet.
  -
  - Multiple readers and writers can have the database open at the same
@@ -118,10 +112,10 @@ runWriter' reconciler a = do
  - the database doesn't exist yet, one caller wins the lock and
  - can create it undisturbed.
  -}
-openDb :: Bool -> (Maybe (SQL.WriteHandle -> Annex ())) -> DbState -> Annex DbState
+openDb :: Bool -> DbState -> Annex DbState
-openDb _ _ st@(DbOpen _) = return st
+openDb _ st@(DbOpen _) = return st
-openDb False _ DbUnavailable = return DbUnavailable
+openDb False DbUnavailable = return DbUnavailable
-openDb forwrite reconciler _ = catchPermissionDenied permerr $ withExclusiveLock gitAnnexKeysDbLock $ do
+openDb forwrite _ = catchPermissionDenied permerr $ withExclusiveLock gitAnnexKeysDbLock $ do
 	dbdir <- fromRepo gitAnnexKeysDb
 	let db = dbdir P.</> "db"
 	dbexists <- liftIO $ R.doesPathExist db
@@ -139,7 +133,7 @@ openDb forwrite reconciler _ = catchPermissionDenied permerr $ withExclusiveLock
 	
 	open db = do
 		qh <- liftIO $ H.openDbQueue H.MultiWriter db SQL.containedTable
-		reconcileStaged qh reconciler
+		reconcileStaged qh
 		return $ DbOpen qh
 
 {- Closes the database if it was open. Any writes will be flushed to it.
@@ -229,8 +223,8 @@ isInodeKnown i s = or <$> runReaderIO ((:[]) <$$> SQL.isInodeKnown i s)
  - So when using getAssociatedFiles, have to make sure the file still
  - is an associated file.
  -}
-reconcileStaged :: H.DbQueue -> Maybe (SQL.WriteHandle -> Annex ()) -> Annex ()
+reconcileStaged :: H.DbQueue -> Annex ()
-reconcileStaged qh mreconciler = do
+reconcileStaged qh = do
 	gitindex <- inRepo currentIndexFile
 	indexcache <- fromRawFilePath <$> fromRepo gitAnnexKeysDbIndexCache
 	withTSDelta (liftIO . genInodeCache gitindex) >>= \case
@@ -252,21 +246,12 @@ reconcileStaged qh mreconciler = do
 	go cur indexcache (Just newtree) = do
 		oldtree <- getoldtree
 		when (oldtree /= newtree) $ do
-			case mreconciler of
-				Just reconciler ->
-					reconciler (SQL.WriteHandle qh)
-				Nothing -> noop
 			g <- Annex.gitRepo
-			void $ catstream $ \mdfeeder -> do
+			void $ catstream $ \mdfeeder -> 
-				case mreconciler of
+				void $ updatetodiff g
-					Nothing -> void $ updatetodiff g
 					(Just (fromRef oldtree)) 
 					(fromRef newtree)
 					(procdiff mdfeeder)
-					Just _ -> void $ updatetodiff g
-						Nothing "--staged"
-						(procdiff mdfeeder)
-
 			liftIO $ writeFile indexcache $ showInodeCache cur
 			-- Storing the tree in a ref makes sure it does not
 			-- get garbage collected, and is available to diff