Combine v and tree internal data structures

[dan-knight]

Related to #120

In clone.out, the node options and tree structure are separated into different dataframes. This can cause issues including:

• Costly and inaccurate lookup (for example. tree[tree$tip == vi$id])
• Inconsistency between index of each data.frame

Since these dataframes both seem to express the same concept - each row representing data for a single subclone - they can likely be combined. This will require further examination, but is worth a look.