make .noannex file prevent repo fixups

Avoid performing repository fixups for submodules and git-worktrees
when there's a .noannex file that will prevent git-annex from being
used in the repository.

This change is ok as long as the .noannex file is really going to prevent
git-annex from being used. But, init --force could override the file.
Which would result in the repo being initialized without the fixups
having run.

To avoid that situation decided to change init, to not let --force be used
to override a .noannex file. Instead the user can just delete the file.

Command/ConfigList.hs

@@ -45,7 +45,7 @@ findOrGenUUID = do
 		else ifM (Annex.Branch.hasSibling <||> (isJust <$> Fields.getField Fields.autoInit))
 			( do
 				liftIO checkNotReadOnly
-				initialize (AutoInit True) Nothing Nothing
+				initialize Nothing Nothing
 				getUUID
 			, return NoUUID
 			)

Command/Init.hs

@@ -52,7 +52,7 @@ start os = do
 
 perform :: InitOptions -> CommandPerform
 perform os = do
-	initialize (AutoInit False)
+	initialize
 		(if null (initDesc os) then Nothing else Just (initDesc os))
 		(initVersion os)
 	Annex.SpecialRemote.autoEnable

Command/Reinit.hs

@@ -36,6 +36,6 @@ perform s = do
 		then return $ toUUID s
 		else Remote.nameToUUID s
 	storeUUID u
-	initialize' (AutoInit False) Nothing
+	initialize' Nothing
 	Annex.SpecialRemote.autoEnable
 	next $ return True

Command/Upgrade.hs

@@ -25,6 +25,6 @@ start :: CommandStart
 start = do
 	showStart' "upgrade" Nothing
 	whenM (isNothing <$> getVersion) $ do
-		initialize (AutoInit False) Nothing Nothing
+		initialize Nothing Nothing
 	r <- upgrade False latestVersion
 	next $ next $ return r