Support removing deleted entries from tree

[andrewherren]

Currently, the tree class handles pruning by marking nodes as "deleted" and thus available for reallocation. This is helpful during training / sampling since the tree class largely consists of vectors and with std::vector, element removal is O(N) but element insertion is (amortized) O(1).

When a tree is done sampling (potentially ready for serialization), it would be nice to re-organize the tree class by removing deleted nodes and renumbering the nodes that remain in the tree::parent_, tree::cleft_, and tree::cright_ vectors.