utils: merkletrie, Fix diff on sparse-checkout index. Fixes #1406

utils/merkletrie/change.go

···
 	}
 
 	if !root.IsDir() {
-		l.Add(ctor(root))
+		if !root.Skip() {
+			l.Add(ctor(root))
+		}
 		return nil
 	}
 

utils/merkletrie/difftree.go

···
 				if err = ret.AddRecursiveDelete(from); err != nil {
 					return nil, err
 				}
-				if err := ii.nextBoth(); err != nil {
-					return nil, err
+				if from.Name() == to.Name() {
+					if err := ii.nextBoth(); err != nil {
+						return nil, err
+					}
+				} else {
+					if err := ii.nextFrom(); err != nil {
+						return nil, err
+					}
 				}
 				break
 			}
···
 				if err = ret.AddRecursiveDelete(to); err != nil {
 					return nil, err
 				}
-				if err := ii.nextBoth(); err != nil {
-					return nil, err
+				if from.Name() == to.Name() {
+					if err := ii.nextBoth(); err != nil {
+						return nil, err
+					}
+				} else {
+					if err := ii.nextTo(); err != nil {
+						return nil, err
+					}
 				}
 				break
 			}

worktree_test.go

···
 	s.True(status.IsClean())
 }
 
+func (s *WorktreeSuite) TestStatusAfterSparseCheckout() {
+	fs := memfs.New()
+	w := &Worktree{
+		r:          s.Repository,
+		Filesystem: fs,
+	}
+
+	err := w.Checkout(&CheckoutOptions{
+		SparseCheckoutDirectories: []string{"php"},
+		Force:                     true,
+	})
+	s.Require().NoError(err)
+
+	status, err := w.Status()
+	s.Require().NoError(err)
+	s.True(status.IsClean(), status)
+}
+
 func (s *WorktreeSuite) TestStatusModified() {
 	fs := s.TemporalFilesystem()