annex.startupscan can be set to false to disable the assistant's startup scan.

Assistant/Threads/Merger.hs

@@ -39,7 +39,7 @@ mergeThread = namedThread "Merger" $ do
 		, modifyHook = changehook
 		, errHook = errhook
 		}
-	void $ liftIO $ watchDir dir (const False) hooks id
+	void $ liftIO $ watchDir dir (const False) True hooks id
 	debug ["watching", dir]
 
 type Handler = FilePath -> Assistant ()

Assistant/Threads/TransferWatcher.hs

@@ -35,7 +35,7 @@ transferWatcherThread = namedThread "TransferWatcher" $ do
 		, modifyHook = modifyhook
 		, errHook = errhook
 		}
-	void $ liftIO $ watchDir dir (const False) hooks id
+	void $ liftIO $ watchDir dir (const False) True hooks id
 	debug ["watching for transfers"]
 
 type Handler = FilePath -> Assistant ()

Assistant/Threads/UpgradeWatcher.hs

@@ -50,8 +50,9 @@ upgradeWatcherThread urlrenderer = namedThread "UpgradeWatcher" $ do
 		let dir = parentDir flagfile
 		let depth = length (splitPath dir) + 1
 		let nosubdirs f = length (splitPath f) == depth
-		void $ liftIO $ watchDir dir nosubdirs hooks (startup mvar)
+		void $ liftIO $ watchDir dir nosubdirs False hooks (startup mvar)
   	-- Ignore bogus events generated during the startup scan.
+	-- We ask the watcher to not generate them, but just to be safe..
   	startup mvar scanner = do
 		r <- scanner
 		void $ swapMVar mvar Started

Assistant/Threads/Watcher.hs

@@ -102,7 +102,8 @@ runWatcher = do
 		, delDirHook = deldirhook
 		, errHook = errhook
 		}
-	handle <- liftIO $ watchDir "." ignored hooks startup
+	scanevents <- liftAnnex $ annexStartupScan <$> Annex.getGitConfig
+	handle <- liftIO $ watchDir "." ignored scanevents hooks startup
 	debug [ "watching", "."]
 	
 	{- Let the DirWatcher thread run until signalled to pause it,