fix restaging of transferred files after stalldetection kicks in

Sponsored-by: Dartmouth College's DANDI project

Annex/Link.hs

@@ -217,6 +217,8 @@ restagePointerFiles r = unlessM (Annex.getState Annex.insmudgecleanfilter) $ do
 	liftIO . Database.Keys.Handle.closeDbHandle
 		=<< Annex.getRead Annex.keysdbhandle
 	realindex <- liftIO $ Git.Index.currentIndexFile r
+	numsz@(numfiles, _) <- calcRestageLog (0, 0) $ \(_f, ic) (numfiles, sizefiles) ->
+		(numfiles+1, sizefiles + inodeCacheFileSize ic)
 	let lock = fromRawFilePath (Git.Index.indexFileLock realindex)
 	    lockindex = liftIO $ catchMaybeIO $ Git.LockFile.openLock' lock
 	    unlockindex = liftIO . maybe noop Git.LockFile.closeLock
@@ -235,8 +237,6 @@ restagePointerFiles r = unlessM (Annex.getState Annex.insmudgecleanfilter) $ do
 				[ Param "-c"
 				, Param $ "core.safecrlf=" ++ boolConfig False
 				] }
-			numsz <- calcRestageLog (0, 0) $ \(_f, ic) (numfiles, sizefiles) ->
-				(numfiles+1, sizefiles + inodeCacheFileSize ic)
 			configfilterprocess numsz $ runsGitAnnexChildProcessViaGit' r'' $ \r''' ->
 				Git.UpdateIndex.refreshIndex r''' $ \feeder -> do
 					let atend = do
@@ -251,7 +251,8 @@ restagePointerFiles r = unlessM (Annex.getState Annex.insmudgecleanfilter) $ do
 		ok <- liftIO (createLinkOrCopy realindex tmpindex)
 			<&&> catchBoolIO updatetmpindex
 		unless ok showwarning
-	bracket lockindex unlockindex go
+	when (numfiles > 0) $
+		bracket lockindex unlockindex go
   where
 	isunmodified tsd f orig = 
 		genInodeCache f tsd >>= return . \case

Annex/TransferrerPool.hs

@@ -1,6 +1,6 @@
 {- A pool of "git-annex transferrer" processes
  -
- - Copyright 2013-2021 Joey Hess <id@joeyh.name>
+ - Copyright 2013-2022 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -22,6 +22,7 @@ import Types.CleanupActions
 import Messages.Serialized
 import Annex.Path
 import Annex.StallDetection
+import Annex.Link
 import Utility.Batch
 import Utility.Metered
 import qualified Utility.SimpleProtocol as Proto
@@ -286,3 +287,10 @@ emptyTransferrerPool = do
 	liftIO $ forM_ pool $ \case
 		TransferrerPoolItem (Just t) _ -> transferrerShutdown t
 		TransferrerPoolItem Nothing _ -> noop
+	-- Transferrers usually restage pointer files themselves,
+	-- but when killTransferrer is used, a transferrer may have
+	-- pointer files it has not gotten around to restaging yet.
+	-- So, restage pointer files here in clean up from such killed
+	-- transferrers.
+	unless (null pool) $
+		restagePointerFiles =<< Annex.gitRepo