go work use -r .
cmp go.work go.work.want

-- go.work --
go 1.18

use (
	.
	./sub
	./sub/dir/deleted
)
-- go.work.want --
go 1.18

use ./sub/dir
-- sub/README.txt --
A go.mod file has been deleted from this directory.
In addition, the entire subdirectory sub/dir/deleted
has been deleted, along with sub/dir/deleted/go.mod.
-- sub/dir/go.mod --
module example/sub/dir
go 1.18
