defer updating unlocked files until after smudge filter

The smuge filter no longer provides git with annexed file content, to
avoid a git memory leak, and because that did not honor annex.thin.

git annex smudge --update has to be run after a checkout to update
unlocked files in the working tree with annexed file contents.

No hooks yet to run it.

This commit was sponsored by Nick Piper on Patreon.

Logs/File.hs

@@ -2,26 +2,59 @@
  -
  - Copyright 2018 Joey Hess <id@joeyh.name>
  -
- - Licensed under the GNU GPL version 3 or higher.
+ - Licensed under the GNU AGPL version 3 or higher.
  -}
 
-module Logs.File where
+module Logs.File (writeLogFile, appendLogFile, streamLogFile) where
 
 import Annex.Common
 import Annex.Perms
+import Annex.LockFile
+import qualified Git
 import Utility.Tmp
 
 -- | Writes content to a file, replacing the file atomically, and
 -- making the new file have whatever permissions the git repository is
 -- configured to use. Creates the parent directory when necessary.
 writeLogFile :: FilePath -> String -> Annex ()
-writeLogFile f c = go `catchNonAsync` \_e -> do
-	-- Most of the time, the directory will exist, so this is only
-	-- done if writing the file fails.
-	createAnnexDirectory (parentDir f)
-	go
+writeLogFile f c = createDirWhenNeeded f $ viaTmp writelog f c
   where
-	go = viaTmp writelog f c
 	writelog f' c' = do
 		liftIO $ writeFile f' c'
 		setAnnexFilePerm f'
+
+-- | Appends a line to a log file, first locking it to prevent
+-- concurrent writers.
+appendLogFile :: FilePath -> (Git.Repo -> FilePath) -> String -> Annex ()
+appendLogFile f lck c = createDirWhenNeeded f $ withExclusiveLock lck $ do
+	liftIO $ withFile f AppendMode $ \h -> hPutStrLn h c
+	setAnnexFilePerm f
+
+-- | Streams lines from a log file, and then empties the file at the end.
+--
+-- If the action is interrupted or throws an exception, the log file is
+-- left unchanged.
+--
+-- Does nothing if the log file does not exist.
+-- 
+-- Locking is used to prevent writes to to the log file while this
+-- is running.
+streamLogFile :: FilePath -> (Git.Repo -> FilePath) -> (String -> Annex ()) -> Annex ()
+streamLogFile f lck a = withExclusiveLock lck $ bracketOnError setup cleanup go
+  where
+	setup = liftIO $ tryWhenExists $ openFile f ReadMode 
+	cleanup Nothing = noop
+	cleanup (Just h) = liftIO $ hClose h
+	go Nothing = noop
+	go (Just h) = do
+		mapM_ a =<< liftIO (lines <$> hGetContents h)
+		liftIO $ hClose h
+		liftIO $ writeFile f ""
+		setAnnexFilePerm f
+
+createDirWhenNeeded :: FilePath -> Annex () -> Annex ()
+createDirWhenNeeded f a = a `catchNonAsync` \_e -> do
+	-- Most of the time, the directory will exist, so this is only
+	-- done if writing the file fails.
+	createAnnexDirectory (parentDir f)
+	a