work around strange auto-init bug

git-annex get when run as the first git-annex command in a new repo did not
populate unlocked files. (Reversion in version 8.20210621)

I am not entirely happy with this, because I don't understand how
428c91606b caused the problem in the first
place, and I don't fully understand how skipping calling scanAnnexedFiles
during autoinit avoids the problem.

Kept the explicit call to scanAnnexedFiles during git-annex init,
so that when reconcileStaged is expensive, it can be made to run then,
rather than at some later point when the information is needed.

Sponsored-by: Brock Spratlen on Patreon

Command/ConfigList.hs

@@ -47,7 +47,7 @@ findOrGenUUID = do
 		else ifM (Annex.Branch.hasSibling <||> (isJust <$> Fields.getField Fields.autoInit))
 			( do
 				liftIO checkNotReadOnly
-				initialize Nothing Nothing
+				initialize True Nothing Nothing
 				getUUID
 			, return NoUUID
 			)

Command/Init.hs

@@ -70,7 +70,7 @@ perform os = do
 			Just v | v /= wantversion ->
 				giveup $ "This repository is already a initialized with version " ++ show (fromRepoVersion v) ++ ", not changing to requested version."
 			_ -> noop
-	initialize
+	initialize False
 		(if null (initDesc os) then Nothing else Just (initDesc os))
 		(initVersion os)
 	Annex.SpecialRemote.autoEnable

Command/Reinit.hs

@@ -35,6 +35,6 @@ perform s = do
 		then return $ toUUID s
 		else Remote.nameToUUID s
 	storeUUID u
-	initialize' Nothing
+	initialize' False Nothing
 	Annex.SpecialRemote.autoEnable
 	next $ return True

Command/Upgrade.hs

@@ -45,6 +45,6 @@ start (UpgradeOptions { autoOnly = True }) =
 start _ =
 	starting "upgrade" (ActionItemOther Nothing) (SeekInput []) $ do
 		whenM (isNothing <$> getVersion) $ do
-			initialize Nothing Nothing
+			initialize False Nothing Nothing
 		r <- upgrade False latestVersion
 		next $ return r