Encapsulate rtree/utree into tree structures

[xflouris]

Current rtree/utree are in fact node structures. Rename them to rnode/unode and encapsulate them. Generic ntree is not necessary at this point of time.

Sample prototype for rooted tree:

typedef struct pll_rtree_s
{
  pll_rnode_t * root;
  pll_rnode_t ** nodes;
  unsigned long tip_count;
  unsigned long inner_count;
  unsigned long branch_count;
} pll_rtree_t;

[xflouris]

encapsulated utree, started work on rtree.

[xflouris]

finished