fix deadlock

Fix a deadlock that could occur after git-annex got an unlocked file,
causing the command to hang indefinitely.

Known to happen on vfat filesystems, possibly others.

Note that a deadlock is still theoretically possible, if anything
smudge --clean does causes it to run the git queue for some other
reason.

Apparently that doesn't happen, but will need to keep an eye on it.

Annex.hs

@@ -151,6 +151,7 @@ data AnnexState = AnnexState
 	, cachedcurrentbranch :: (Maybe (Maybe Git.Branch, Maybe Adjustment))
 	, cachedgitenv :: Maybe (AltIndexFile, FilePath, [(String, String)])
 	, urloptions :: Maybe UrlOptions
+	, insmudgecleanfilter :: Bool
 	}
 
 newState :: GitConfig -> Git.Repo -> IO AnnexState
@@ -209,6 +210,7 @@ newState c r = do
 		, cachedcurrentbranch = Nothing
 		, cachedgitenv = Nothing
 		, urloptions = Nothing
+		, insmudgecleanfilter = False
 		}
 
 {- Makes an Annex state object for the specified git repo.

Annex/Link.hs

@@ -177,7 +177,13 @@ newtype Restage = Restage Bool
 restagePointerFile :: Restage -> RawFilePath -> InodeCache -> Annex ()
 restagePointerFile (Restage False) f _ =
 	toplevelWarning True $ unableToRestage $ Just $ fromRawFilePath f
-restagePointerFile (Restage True) f orig = withTSDelta $ \tsd -> do
+restagePointerFile (Restage True) f orig = withTSDelta $ \tsd ->
+	-- Avoid refreshing the index if run by the
+	-- smudge clean filter, because git uses that when
+	-- it's already refreshing the index, probably because
+	-- this very action is running. Running it again would likely
+	-- deadlock.
+	unlessM (Annex.getState Annex.insmudgecleanfilter) $ do
 		-- update-index is documented as picky about "./file" and it
 		-- fails on "../../repo/path/file" when cwd is not in the repo 
 		-- being acted on. Avoid these problems with an absolute path.

CHANGELOG

@@ -1,3 +1,11 @@
+git-annex (8.20200618) UNRELEASED; urgency=medium
+
+  * Fix a deadlock that could occur after git-annex got an unlocked
+    file, causing the command to hang indefinitely. Known to happen on 
+    vfat filesystems, possibly others.
+
+ -- Joey Hess <id@joeyh.name>  Thu, 18 Jun 2020 12:21:14 -0400
+
 git-annex (8.20200617) upstream; urgency=medium
 
   * Added annex.skipunknown git config, that can be set to false to change

Command/Smudge.hs

@@ -88,18 +88,23 @@ clean file = do
 	b <- liftIO $ L.hGetContents stdin
 	ifM fileoutsiderepo
 		( liftIO $ L.hPut stdout b
-		, case parseLinkTargetOrPointerLazy b of
+		, do
+			-- Avoid a potential deadlock.
+			Annex.changeState $ \s -> s
+				{ Annex.insmudgecleanfilter = True }
+			go b
+		)
+	stop
+  where
+	go b = case parseLinkTargetOrPointerLazy b of
 		Just k -> do
 			getMoveRaceRecovery k (toRawFilePath file)
 			liftIO $ L.hPut stdout b
 		Nothing -> do
 			let fileref = Git.Ref.fileRef (toRawFilePath file)
 			indexmeta <- catObjectMetaData fileref
-				go b indexmeta =<< catKey' fileref indexmeta
+			go' b indexmeta =<< catKey' fileref indexmeta
-		)
+	go' b indexmeta oldkey = ifM (shouldAnnex file indexmeta oldkey)
-	stop
-  where
-	go b indexmeta oldkey = ifM (shouldAnnex file indexmeta oldkey)
 		( do
 			-- Before git 2.5, failing to consume all stdin here
 			-- would cause a SIGPIPE and crash it.