commit git-annex branch when copying to a remote (locally)

Otherwise, the location log changes are only staged in its index,
and this can confuse matters if pulling or cloning from the remote.

The test suite was failing because this wasn't done.

CmdLine.hs

@@ -19,7 +19,7 @@ import Control.Monad (when)
 import qualified Annex
 import qualified AnnexQueue
 import qualified GitRepo as Git
-import qualified Branch
+import Content
 import Types
 import Command
 import BackendList
@@ -103,9 +103,6 @@ startup = do
 {- Cleanup actions. -}
 shutdown :: Annex Bool
 shutdown = do
-	AnnexQueue.flush False
+	saveState
-	Branch.commit "update"
-
 	liftIO $ Git.reap
-	
 	return True

Content.hs

@@ -19,7 +19,8 @@ module Content (
 	removeAnnex,
 	fromAnnex,
 	moveBad,
-	getKeysPresent
+	getKeysPresent,
+	saveState
 ) where
 
 import System.IO.Error (try)
@@ -37,6 +38,8 @@ import LocationLog
 import UUID
 import qualified GitRepo as Git
 import qualified Annex
+import qualified AnnexQueue
+import qualified Branch
 import Utility
 import StatFS
 import Types.Key
@@ -263,3 +266,9 @@ getKeysPresent' dir = do
 			case result of
 				Right s -> return $ isRegularFile s
 				Left _ -> return False
+
+{- Things to do to record changes to content. -}
+saveState :: Annex ()
+saveState = do
+	AnnexQueue.flush False
+	Branch.commit "update"

Remote/Git.hs

@@ -17,7 +17,6 @@ import Types
 import Types.Remote
 import qualified GitRepo as Git
 import qualified Annex
-import qualified AnnexQueue
 import Locations
 import UUID
 import Utility
@@ -147,7 +146,7 @@ copyToRemote r key
 			Annex.eval a $ do
 				ok <- Content.getViaTmp key $
 					rsyncOrCopyFile r keysrc
-				AnnexQueue.flush True
+				Content.saveState
 				return ok
 	| Git.repoIsSsh r = do
 		g <- Annex.gitRepo