Moved function for simulating coalescence times for a single tumour to a separate file.

This function will be used in simulation of other cases so shouldn't be a part of the single-tumour simulation file.
updated ignored files
Removed some example Rcpp files I don't need any longer.
Fixed the math for sampling TA
Save root edge with t1 represented
Plot with root edge
Times are simulated slightly wrong in case B, but I commit anyway so I can continue work at the office...
Updated sampling of TA to the math from coalescent_v5.pdf
Still some problems with sampling times for case B, but committing to continue at home...
Experiments with the sampler and a hybrid sampler
Bugfix in simulation. rcoal wants difference in times not the absolute coalescence times
Sampling of two tumours. I don't know if it is the plot code or the tree.bind code that gives me the wrong tau offset some times...
Fixed sampling of conditional sampling trees and merging into a joint tree.
Merge branch 'feature/case_B' into develop