assistant: Fix race in v6 mode that caused downloaded file content to sometimes not replace pointer files.

The keys database handle needs to be closed after merging, because the
smudge filter, in another process, updates the database. Old cached info
can be read for a while from the open database handle; closing it ensures
that the info written by the smudge filter is available.

This is pretty horribly ad-hoc, and it's especially nasty that the
transferrer closes the database every time.

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