diff --git a/Annex/Init.hs b/Annex/Init.hs
index 962eae26eb..adbee09333 100644
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -135,7 +135,7 @@ initialize' mversion = checkInitializeAllowed $ do
 		then configureSmudgeFilter
 		else deconfigureSmudgeFilter
 	unlessM isBareRepo $ do
-		scanAnnexedFiles True
+		scanAnnexedFiles
 		hookWrite postCheckoutHook
 		hookWrite postMergeHook
 	AdjustedBranch.checkAdjustedClone >>= \case
diff --git a/Annex/WorkTree.hs b/Annex/WorkTree.hs
index 60b460e813..7bb4b9fe00 100644
--- a/Annex/WorkTree.hs
+++ b/Annex/WorkTree.hs
@@ -8,24 +8,10 @@
 module Annex.WorkTree where
 
 import Annex.Common
-import qualified Annex
 import Annex.Link
 import Annex.CatFile
-import Annex.Content
-import Annex.ReplaceFile
 import Annex.CurrentBranch
-import Annex.InodeSentinal
-import Utility.InodeCache
-import Git.FilePath
-import Git.CatFile
-import qualified Git.Ref
-import qualified Git.LsTree
-import qualified Git.Types
 import qualified Database.Keys
-import Config
-import qualified Utility.RawFilePath as R
-
-import qualified Data.ByteString.Lazy as L
 
 {- Looks up the key corresponding to an annexed file in the work tree,
  - by examining what the file links to.
@@ -69,74 +55,13 @@ ifAnnexed file yes no = maybe no yes =<< lookupKey file
 
 {- Find all annexed files and update the keys database for them.
  - 
- - This is expensive, and so normally the associated files are updated
- - incrementally when changes are noticed. So, this only needs to be done
- - when initializing/upgrading a repository.
- -
- - Also, the content for an unlocked file may already be present as
- - an annex object. If so, populate the pointer file with it.
- - But if worktree file does not have a pointer file's content, it is left
- - as-is.
+ - Normally the keys database is updated incrementally when it's being
+ - opened, and changes are noticed. Calling this explicitly allows
+ - running the update at an earlier point.
  -}
-scanAnnexedFiles :: Bool -> Annex ()
-scanAnnexedFiles initscan = do
-	-- This gets the keys database populated with all annexed files,
-	-- by running Database.Keys.reconcileStaged.
+scanAnnexedFiles :: Annex ()
+scanAnnexedFiles =
+	-- All that needs to be done is to open the database,
+	-- that will result in Database.Keys.reconcileStaged
+	-- running, and doing the work.
 	Database.Keys.runWriter (const noop)
-	-- The above tries to populate pointer files, but one thing it
-	-- is not able to handle is populating a pointer file when the
-	-- annex object file already exists, but its inode is not yet
-	-- cached and annex.thin is set. So, the rest of this makes
-	-- another pass over the tree to do that.
-	whenM
-		( pure initscan
-		<&&> annexThin <$> Annex.getGitConfig
-		<&&> inRepo Git.Ref.headExists
-		<&&> not <$> isBareRepo
-		) $ do
-			g <- Annex.gitRepo
-			(l, cleanup) <- inRepo $ Git.LsTree.lsTree
-				Git.LsTree.LsTreeRecursive
-				(Git.LsTree.LsTreeLong True)
-				Git.Ref.headRef
-			catObjectStreamLsTree l want g go
-			liftIO $ void cleanup
-  where
-	-- Want to process symlinks, and regular files.
-	want i = case Git.Types.toTreeItemType (Git.LsTree.mode i) of
-		Just Git.Types.TreeSymlink -> Just (i, False)
-		Just Git.Types.TreeFile -> checkfilesize i
-		Just Git.Types.TreeExecutable -> checkfilesize i
-		_ -> Nothing
-	
-	-- Avoid processing files that are too large to be pointer files.
-	checkfilesize i = case Git.LsTree.size i of
-		Just n | n < maxPointerSz -> Just (i, True)
-		_ -> Nothing
-	
-	go getnext = liftIO getnext >>= \case
-		Just ((i, isregfile), Just c) -> do
-			maybe noop (add i isregfile)
-				(parseLinkTargetOrPointer (L.toStrict c))
-			go getnext
-		_ -> return ()
-	
-	add i isregfile k = do
-		let tf = Git.LsTree.file i
-		whenM (pure isregfile <&&> inAnnex k) $ do
-			f <- fromRepo $ fromTopFilePath tf
-			liftIO (isPointerFile f) >>= \case
-				Just k' | k' == k -> do
-					destmode <- liftIO $ catchMaybeIO $
-						fileMode <$> R.getFileStatus f
-					ic <- replaceWorkTreeFile (fromRawFilePath f) $ \tmp -> do
-						let tmp' = toRawFilePath tmp
-						linkFromAnnex' k tmp' destmode >>= \case
-							LinkAnnexOk -> 
-								withTSDelta (liftIO . genInodeCache tmp')
-							LinkAnnexNoop -> return Nothing
-							LinkAnnexFailed -> liftIO $ do
-								writePointerFile tmp' k destmode
-								return Nothing
-					maybe noop (restagePointerFile (Restage True) f) ic
-				_ -> noop
diff --git a/Command/Smudge.hs b/Command/Smudge.hs
index 70fc9235ad..c242b7e1b5 100644
--- a/Command/Smudge.hs
+++ b/Command/Smudge.hs
@@ -267,7 +267,7 @@ update = do
 	-- point to refresh the keys database for changes to annexed files.
 	-- Doing it explicitly here avoids a later pause in the middle of
 	-- some other action.
-	scanAnnexedFiles False
+	scanAnnexedFiles
 	updateSmudged (Restage True)
 	stop
 
diff --git a/Upgrade/V5.hs b/Upgrade/V5.hs
index 22200b0c80..2db92d57f9 100644
--- a/Upgrade/V5.hs
+++ b/Upgrade/V5.hs
@@ -47,7 +47,7 @@ upgrade automatic = flip catchNonAsync onexception $ do
 		, do
 			checkGitVersionForIndirectUpgrade
 		)
-	scanAnnexedFiles True
+	scanAnnexedFiles
 	configureSmudgeFilter
 	-- Inode sentinal file was only used in direct mode and when
 	-- locking down files as they were added. In v6, it's used more