Revert "refactor: Alternative way to set the initialversion root node"

This reverts commit 6365e4e.

Adding this just so we have reference of the other option

mutable_tree.go

@@ -787,6 +787,23 @@ func (tree *MutableTree) SaveVersion() ([]byte, int64, error) {
 			if err := tree.ndb.SaveRoot(version, tree.root.nodeKey); err != nil {
 				return nil, 0, err
 			}
+
+			// Delete the root node to be replaced below with new key. Need to
+			// delete this otherwise there will be two keys (version, 1) and
+			// (version, 0) below pointing at the same node.
+			if err := tree.ndb.deleteFromPruning(tree.ndb.nodeKey(tree.root.nodeKey.GetKey())); err != nil {
+				return nil, 0, err
+			}
+
+			// Use a nonce of 0 to match pruning behavior that hides it from
+			// the version list.
+			// Mark the root node as hidden, same as how pruning handles.
+			// Even if with the reference node via SaveRoot() above points at
+			// (version, 1), LoadVersion still checks (version, 0) if it exists.
+			tree.root.nodeKey.nonce = 0
+			if err := tree.ndb.SaveNode(tree.root); err != nil {
+				return nil, 0, err
+			}
 		}
 	}
 
@@ -1051,9 +1068,6 @@ func (tree *MutableTree) balance(node *Node) (newSelf *Node, err error) {
 func (tree *MutableTree) saveNewNodes() error {
 	nonce := uint32(0)
 	newNodes := make([]*Node, 0)
-
-	isInitialVersion := tree.ndb.opts.InitialVersion > 1 && tree.WorkingVersion() == int64(tree.ndb.opts.InitialVersion)
-
 	var recursiveAssignKey func(*Node) ([]byte, error)
 	recursiveAssignKey = func(node *Node) ([]byte, error) {
 		if node.nodeKey != nil {
@@ -1067,12 +1081,6 @@ func (tree *MutableTree) saveNewNodes() error {
 			nonce:   nonce,
 		}
 
-		// Save the root node at InitialVersion to nonce of 0 to hide it from
-		// the version list.
-		if isInitialVersion && nonce == 1 {
-			node.nodeKey.nonce = 0
-		}
-
 		var err error
 		// the inner nodes should have two children.
 		if node.subtreeHeight > 0 {