have clean filter check if the filename was already in use by an old key

The annex object for it may have been modified due to hard link, and
that should be cleaned up when the new version is added. If another
associated file has the old key's content, that's linked into the annex
object. Otherwise, update location log to reflect that content has been
lost.

Command/Smudge.hs

@@ -13,6 +13,7 @@ import Annex.Content
 import Annex.Link
 import Annex.MetaData
 import Annex.FileMatcher
+import Annex.InodeSentinal
 import Types.KeySource
 import Backend
 import Logs.Location
@@ -51,7 +52,7 @@ smudge file = do
 			-- A previous unlocked checkout of the file may have
 			-- led to the annex object getting modified;
 			-- don't provide such modified content as it
-			-- will be confusing. inAnnex will detect
+			-- will be confusing. inAnnex will detect such
 			-- modifications.
 			ifM (inAnnex k)
 				( do
@@ -74,12 +75,35 @@ clean file = do
 		else ifM (shouldAnnex file)
 			( do
 				k <- ingest file
+				oldkeys <- filter (/= k)
+					<$> Database.Keys.getAssociatedKey file
+				mapM_ (cleanOldKey file) oldkeys
 				Database.Keys.addAssociatedFile k file
 				liftIO $ emitPointer k
 			, liftIO $ B.hPut stdout b
 			)
 	stop
 
+-- If the file being cleaned was hard linked to the old key's annex object,
+-- modifying the file will have caused the object to have the wrong content.
+-- Clean up from that, making the 
+cleanOldKey :: FilePath -> Key -> Annex ()
+cleanOldKey modifiedfile key = do
+	obj <- calcRepo (gitAnnexLocation key)
+	caches <- Database.Keys.getInodeCaches key
+	unlessM (sameInodeCache obj caches) $ do
+		unlinkAnnex key
+		fs <- filter (/= modifiedfile)
+			<$> Database.Keys.getAssociatedFiles key
+		fs' <- filterM (`sameInodeCache` caches) fs
+		case fs' of
+			-- If linkAnnex fails, the file with the content
+			-- is still present, so no need for any recovery.
+			(f:_) -> void $ linkAnnex key f
+			_ -> lostcontent
+  where
+	lostcontent = logStatus key InfoMissing
+
 shouldAnnex :: FilePath -> Annex Bool
 shouldAnnex file = do
 	matcher <- largeFilesMatcher

doc/todo/smudge.mdwn

@@ -325,9 +325,6 @@ files to be unlocked, while the indirect upgrades don't touch the files.
   because the timestamp has changed. Getting a smudged file can also 
   cause this. Avoid this by preserving timestamp of smudged files
   when manipulating.
-* Clean filter should check if the filename was already in use by an old
-  key. The annex object for it may have been modified due to hard link, and
-  that should be cleaned up when the new version is added.
 * Reconcile staged changes into the associated files database, whenever
   the database is queried.
 * See if the cases where the Keys database is not used can be