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.

Command/LookupKey.hs

@@ -31,7 +31,7 @@ run _ file = seekSingleGitFile file >>= \case
 -- But, this plumbing command does not recurse through directories.
 seekSingleGitFile :: FilePath -> Annex (Maybe RawFilePath)
 seekSingleGitFile file = do
-	(l, cleanup) <- inRepo (Git.LsFiles.inRepo [toRawFilePath file])
+	(l, cleanup) <- inRepo (Git.LsFiles.inRepo [] [toRawFilePath file])
 	r <- case l of
 		(f:[]) | takeFileName (fromRawFilePath f) == takeFileName file ->
 			return (Just f)