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

Command/Smudge.hs

@@ -13,6 +13,7 @@ import Annex.Link
 import Annex.FileMatcher
 import Annex.Ingest
 import Annex.CatFile
+import Annex.WorkTree
 import Logs.Smudge
 import Logs.Location
 import qualified Database.Keys
@@ -262,6 +263,11 @@ getMoveRaceRecovery k file = void $ tryNonAsync $
 
 update :: CommandStart
 update = do
+	-- This gets run after a git checkout or merge, so it's a good
+	-- 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
 	updateSmudged (Restage True)
 	stop