7 files changed, 70 insertions, 13 deletions
diff --git a/Assistant/Threads/Merger.hs b/Assistant/Threads/Merger.hs
index 521e5bda6..0080ef964 100644
--- a/Assistant/Threads/Merger.hs
+++ b/Assistant/Threads/Merger.hs
@@ -19,6 +19,7 @@ import qualified Annex.Branch
 import qualified Git
 import qualified Git.Branch
 import qualified Command.Sync
+import qualified Database.Keys
 import Annex.TaggedPush
 import Remote (remoteFromUUID)
 
@@ -89,6 +90,12 @@ onChange file
 					currbranch mergeConfig
 					Git.Branch.AutomaticCommit
 					changedbranch
+				-- Merging can cause new associated files
+				-- to appear and the smudge filter will
+				-- add them to the database. To ensure that
+				-- this process sees those changes, close
+				-- the database if it was open.
+				liftAnnex $ Database.Keys.closeDb
 	mergecurrent _ = noop
 
 	handleDesynced = case fromTaggedBranch changedbranch of
diff --git a/Assistant/Threads/Watcher.hs b/Assistant/Threads/Watcher.hs
index f0a639984..1f50065b9 100644
--- a/Assistant/Threads/Watcher.hs
+++ b/Assistant/Threads/Watcher.hs
@@ -221,7 +221,11 @@ shouldRestage :: DaemonStatus -> Bool
 shouldRestage ds = scanComplete ds || forceRestage ds
 
 onAddUnlocked :: Bool -> GetFileMatcher -> Handler
-onAddUnlocked = onAddUnlocked' False contentchanged addassociatedfile samefilestatus
+onAddUnlocked symlinkssupported matcher f fs = do
+	mk <- liftIO $ isPointerFile f
+	case mk of
+		Nothing -> onAddUnlocked' False contentchanged addassociatedfile addlink samefilestatus symlinkssupported matcher f fs
+		Just k -> addlink f k
   where
 	addassociatedfile key file = 
 		Database.Keys.addAssociatedFile key
@@ -238,15 +242,32 @@ onAddUnlocked = onAddUnlocked' False contentchanged addassociatedfile samefilest
 			=<< inRepo (toTopFilePath file)
 		unlessM (inAnnex oldkey) $
 			logStatus oldkey InfoMissing
+	addlink file key = do
+		mode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus file
+		liftAnnex $ stagePointerFile file mode =<< hashPointerFile key
+		madeChange file $ LinkChange (Just key)
 
 {- In direct mode, add events are received for both new files, and
  - modified existing files.
  -}
 onAddDirect :: Bool -> GetFileMatcher -> Handler
-onAddDirect = onAddUnlocked' True changedDirect (\k f -> void $ addAssociatedFile k f) sameFileStatus
-
-onAddUnlocked' :: Bool -> (Key -> FilePath -> Annex ()) -> (Key -> FilePath -> Annex ()) -> (Key -> FilePath -> FileStatus -> Annex Bool) -> Bool -> GetFileMatcher -> Handler
-onAddUnlocked' isdirect contentchanged addassociatedfile samefilestatus symlinkssupported matcher file fs = do
+onAddDirect = onAddUnlocked' True changedDirect addassociatedfile addlink sameFileStatus
+  where
+	addassociatedfile key file = void $ addAssociatedFile key file
+	addlink file key = do
+		link <- liftAnnex $ calcRepo $ gitAnnexLink file key
+		addLink file link (Just key)
+
+onAddUnlocked'
+	:: Bool
+	-> (Key -> FilePath -> Annex ())
+	-> (Key -> FilePath -> Annex ())
+	-> (FilePath -> Key -> Assistant (Maybe Change))
+	-> (Key -> FilePath -> FileStatus -> Annex Bool)
+	-> Bool
+	-> GetFileMatcher
+	-> Handler
+onAddUnlocked' isdirect contentchanged addassociatedfile addlink samefilestatus symlinkssupported matcher file fs = do
 	v <- liftAnnex $ catKeyFile file
 	case (v, fs) of
 		(Just key, Just filestatus) ->
@@ -255,11 +276,9 @@ onAddUnlocked' isdirect contentchanged addassociatedfile samefilestatus symlinks
 				 - an existing file that is not
 				 - really modified, but it might have
 				 - just been deleted and been put back,
-				 - so it symlink is restaged to make sure. -}
+				 - so its annex link is restaged to make sure. -}
 				( ifM (shouldRestage <$> getDaemonStatus)
-					( do
-						link <- liftAnnex $ calcRepo $ gitAnnexLink file key
-						addLink file link (Just key)
+					( addlink file key
 					, noChange
 					)
 				, guardSymlinkStandin (Just key) $ do
diff --git a/Command/TransferKeys.hs b/Command/TransferKeys.hs
index 005e491b4..82dc15032 100644
--- a/Command/TransferKeys.hs
+++ b/Command/TransferKeys.hs
@@ -16,6 +16,7 @@ import Annex.Transfer
 import qualified Remote
 import Utility.SimpleProtocol (dupIoHandles)
 import Git.Types (RemoteName)
+import qualified Database.Keys
 
 data TransferRequest = TransferRequest Direction Remote Key AssociatedFile
 
@@ -41,8 +42,13 @@ start = do
 				return ok
 		| otherwise = notifyTransfer direction file $
 			download (Remote.uuid remote) key file forwardRetry observer $ \p ->
-				getViaTmp (RemoteVerify remote) key $ \t -> 
-					Remote.retrieveKeyFile remote key file t p
+				getViaTmp (RemoteVerify remote) key $ \t -> do
+					r <- Remote.retrieveKeyFile remote key file t p
+					-- Make sure we get the current
+					-- associated files data for the key,
+					-- not old cached data.
+					Database.Keys.closeDb			
+					return r
 	
 	observer False t tinfo = recordFailedTransfer t tinfo
 	observer True _ _ = noop
diff --git a/Database/Keys.hs b/Database/Keys.hs
index ed3878161..778540137 100644
--- a/Database/Keys.hs
+++ b/Database/Keys.hs
@@ -9,6 +9,7 @@
 
 module Database.Keys (
 	DbHandle,
+	closeDb,
 	addAssociatedFile,
 	getAssociatedFiles,
 	getAssociatedKey,
@@ -137,6 +138,16 @@ openDb createdb _ = catchPermissionDenied permerr $ withExclusiveLock gitAnnexKe
 		False -> return DbUnavailable
 		True -> throwM e
 
+{- Closes the database if it was open. Any writes will be flushed to it.
+ -
+ - This does not normally need to be called; the database will auto-close
+ - when the handle is garbage collected. However, this can be used to
+ - force a re-read of the database, in case another process has written
+ - data to it.
+ -}
+closeDb :: Annex ()
+closeDb = liftIO . closeDbHandle =<< getDbHandle
+
 addAssociatedFile :: Key -> TopFilePath -> Annex ()
 addAssociatedFile k f = runWriterIO $ SQL.addAssociatedFile (toIKey k) f
 
diff --git a/Database/Keys/Handle.hs b/Database/Keys/Handle.hs
index 51de58fa8..1ef16d031 100644
--- a/Database/Keys/Handle.hs
+++ b/Database/Keys/Handle.hs
@@ -11,6 +11,7 @@ module Database.Keys.Handle (
 	DbState(..),
 	withDbState,
 	flushDbQueue,
+	closeDbHandle,
 ) where
 
 import qualified Database.Queue as H
@@ -38,8 +39,7 @@ newDbHandle = DbHandle <$> newMVar DbClosed
 withDbState
 	:: (MonadIO m, MonadCatch m)
 	=> DbHandle
-	-> (DbState
-	-> m (v, DbState))
+	-> (DbState -> m (v, DbState))
 	-> m v
 withDbState (DbHandle mvar) a = do
 	st <- liftIO $ takeMVar mvar
@@ -55,3 +55,11 @@ flushDbQueue (DbHandle mvar) = go =<< readMVar mvar
   where
 	go (DbOpen qh) = H.flushDbQueue qh
 	go _ = return ()
+
+closeDbHandle :: DbHandle -> IO ()
+closeDbHandle h = withDbState h go
+  where
+	go (DbOpen qh) = do
+		H.closeDbQueue qh
+		return ((), DbClosed)
+	go st = return ((), st)
diff --git a/debian/changelog b/debian/changelog
index a653efdfd..e9de8bce8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,10 @@ git-annex (6.20160512) UNRELEASED; urgency=medium
   * adjust: If the adjusted branch already exists, avoid overwriting it,
     since it might contain changes that have not yet been propigated to the
     original branch.
+  * assistant: Fix bug that caused v6 pointer files to be annexed by the
+    assistant.
+  * assistant: Fix race in v6 mode that caused downloaded file content to
+    sometimes not replace pointer files.
 
  -- Joey Hess <id@joeyh.name>  Wed, 11 May 2016 16:08:38 -0400
 
diff --git a/doc/bugs/Central_annex_+_assistant_+_v6___61___weirdness__63__.mdwn b/doc/bugs/Central_annex_+_assistant_+_v6___61___weirdness__63__.mdwn
index 5afd3d31a..4acf81e7b 100644
--- a/doc/bugs/Central_annex_+_assistant_+_v6___61___weirdness__63__.mdwn
+++ b/doc/bugs/Central_annex_+_assistant_+_v6___61___weirdness__63__.mdwn
@@ -102,3 +102,5 @@ Everything up-to-date
 
 ### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
 It seems to work really well on v5, but the v6 file "corruption" is difficult to recover from.
+
+> [[fixed|done]] --[[Joey]]