Add cstdlib include file in Log.cpp
Improve loading event data from previous run

The input format for loading events has changed. It is now identical to the
output event format, so that the user can simply use that output file as input.
Only the data from the last generation will be used.
Make the Settings object be passed by reference
Make Tree node list a vector and re-arrange code
Convert nodes and downpass nodes into traversals

In class Tree, nodes was a set and downpassSeq was a vector. They are
now both vectors and have been renamed to reflect the type of traversal
(pre-order or post-order) that they are.
Remove _ntaxa (not used anywhere)
Move more tree-reading code to readTree method
Change setNodeTimes to use pre-order traversal
Rewrite Tree::setAge() using an algorithm function
Refactor log-likelihood calculation in SpExModel
Merge branch 'mcmc-refactor-mc3' into time-var-const

Conflicts:
	src/SpExModel.cpp
	src/SpExModel.h