annex.skipunknown with transition plan

Added annex.skipunknown git config, that can be set to false to change the
behavior of commands like `git annex get foo*`, to not skip over files/dirs
that are not checked into git and are explicitly listed in the command
line.

Significant complexity was needed to handle git-annex add, which uses some
git ls-files calls, but needs to not use --error-unmatch because of course
the files are not known to git.

annex.skipunknown is planned to change to default to false in a
git-annex release in early 2022. There's a todo for that.

Assistant/Threads/TransferScanner.hs

@@ -128,7 +128,7 @@ expensiveScan urlrenderer rs = batch <~> do
 		<$> filterM inUnwantedGroup us
 
 	g <- liftAnnex gitRepo
-	(files, cleanup) <- liftIO $ LsFiles.inRepo [] g
+	(files, cleanup) <- liftIO $ LsFiles.inRepo [] [] g
 	removablers <- scan unwantedrs files
 	void $ liftIO cleanup