diff --git a/Assistant/Threads/Committer.hs b/Assistant/Threads/Committer.hs
index 75976ee3ce..99d01b5804 100644
--- a/Assistant/Threads/Committer.hs
+++ b/Assistant/Threads/Committer.hs
@@ -82,8 +82,7 @@ commitStaged = do
 		Right _ -> do
 			direct <- isDirect
 			let params = nomessage $ catMaybes
-				[ Just $ Param "-c", Just $ Param "gc.auto=0"
-				, Just $ Param "commit"
+				[ Just $ Param "commit"
 				, Just $ Param "--quiet"
 				{- In indirect mode, avoid running the
 				 - usual git-annex pre-commit hook;
diff --git a/Assistant/Threads/SanityChecker.hs b/Assistant/Threads/SanityChecker.hs
index 8064410585..906167ca87 100644
--- a/Assistant/Threads/SanityChecker.hs
+++ b/Assistant/Threads/SanityChecker.hs
@@ -15,6 +15,7 @@ import Assistant.DaemonStatus
 import Assistant.Alert
 import qualified Git.LsFiles
 import qualified Git.Command
+import qualified Git.Config
 import Utility.ThreadScheduler
 import qualified Assistant.Threads.Watcher as Watcher
 import Utility.LogFile
@@ -85,8 +86,16 @@ dailyCheck = do
 	liftIO $ void cleanup
 
 	{- Allow git-gc to run once per day. More frequent gc is avoided
-	 - to avoid slowing things down. -}
-	void $ liftIO $ Git.Command.runBool [Param "gc", Param "--auto"] g
+	 - by default to avoid slowing things down. Only run repacks when 100x
+	 - the usual number of loose objects are present; we tend
+	 - to have a lot of small objects and they should not be a
+	 - significant size. -}
+	when (Git.Config.getMaybe "gc.auto" g == Just "0") $
+		liftIO $ void $ Git.Command.runBool
+			[ Param "-c", Param "gc.auto=670000"
+			, Param "gc"
+			, Param "--auto"
+			] g
 
 	return True
   where
diff --git a/Assistant/WebApp/Configurators/Local.hs b/Assistant/WebApp/Configurators/Local.hs
index eb2a6cb661..53bd95d012 100644
--- a/Assistant/WebApp/Configurators/Local.hs
+++ b/Assistant/WebApp/Configurators/Local.hs
@@ -302,9 +302,9 @@ initRepo primary_assistant_repo dir desc = inDir dir $ do
 	{- Initialize a git-annex repository in a directory with a description. -}
 	unlessM isInitialized $
 		initialize desc
+	{- Initialize the master branch, so things that expect
+	 - to have it will work, before any files are added. -}
 	unlessM (Git.Config.isBare <$> gitRepo) $
-		{- Initialize the master branch, so things that expect
-		 - to have it will work, before any files are added. -}
 		void $ inRepo $ Git.Command.runBool
 			[ Param "commit"
 			, Param "--quiet"
@@ -312,8 +312,15 @@ initRepo primary_assistant_repo dir desc = inDir dir $ do
 			, Param "-m"
 			, Param "created repository"
 			]
-	when primary_assistant_repo $
+	{- Repositories directly managed by the assistant use direct mode.
+	 - 
+	 - Automatic gc is disabled, as it can be slow. Insted, gc is done
+	 - once a day.
+	 -}
+	when primary_assistant_repo $ do
 		setDirect True
+		inRepo $ Git.Command.run
+			[Param "config", Param "gc.auto", Param "0"]
 	getUUID
 
 {- Adds a directory to the autostart file. -}
diff --git a/debian/changelog b/debian/changelog
index a9a0fc10af..dab3e7b5ba 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -9,9 +9,10 @@ git-annex (4.20130228) UNRELEASED; urgency=low
     files in direct mode repositories.
   * assistant: Fix dropping content when a file is moved to an archive
     directory.
-  * assistant: Prevent automatic commits from causing git-gc runs,
-    as that can make things quite slow. Instead, git-gc --auto is run
-    once a day. (This can be disabled by the usual gc.auto=0 setting.)
+  * assistant: Set gc.auto=0 when creating repositories to prevent
+    automatic commits from causing git-gc runs.
+  * assistant: If gc.auto=0, run git-gc once a day, packing loose objects
+    very non-aggressively.
 
  -- Joey Hess <joeyh@debian.org>  Wed, 27 Feb 2013 23:20:40 -0400