scanAnnexedFiles in smudge --update

This makes git checkout and git merge hooks do the work to catch up with
changes that they made to the tree. Rather than doing it at some later
point when the user is not thinking about that past operation.

Sponsored-by: Dartmouth College's Datalad project

Annex/WorkTree.hs

@@ -15,6 +15,8 @@ import Annex.Content
 import Annex.ReplaceFile
 import Annex.CurrentBranch
 import Annex.InodeSentinal
+import Annex.Concurrent
+import Utility.ThreadScheduler
 import Utility.InodeCache
 import Git.FilePath
 import Git.CatFile
@@ -78,8 +80,8 @@ ifAnnexed file yes no = maybe no yes =<< lookupKey file
  - But if worktree file does not have a pointer file's content, it is left
  - as-is.
  -}
-scanAnnexedFiles :: Annex ()
-scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ do
+scanAnnexedFiles :: Bool -> Annex ()
+scanAnnexedFiles initscan = showSideActionAfter oneSecond "scanning for annexed files" $ do
 	-- This gets the keys database populated with all annexed files,
 	-- by running Database.Keys.reconcileStaged.
 	Database.Keys.runWriter (const noop)
@@ -88,14 +90,19 @@ scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ d
 	-- 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 (annexThin <$> Annex.getGitConfig) $ 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
+	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