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/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