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/SanityChecker.hs

@@ -152,7 +152,7 @@ dailyCheck urlrenderer = do
 	batchmaker <- liftIO getBatchCommandMaker
 
 	-- Find old unstaged symlinks, and add them to git.
-	(unstaged, cleanup) <- liftIO $ Git.LsFiles.notInRepo False ["."] g
+	(unstaged, cleanup) <- liftIO $ Git.LsFiles.notInRepo [] False ["."] g
 	now <- liftIO getPOSIXTime
 	forM_ unstaged $ \file -> do
 		let file' = fromRawFilePath file