Fix: Set mean branch parameters after setting root
Add a set method to Settings
Make some priors not required
Add isUserDefined method to Settings
Make possionRatePrior optional
Make initial parameters in Settings optional
Add setIfUserDefined method to Settings
Make an infinite initial log-likelihood a Warning

It was an error, but exiting the program does not allow the model class
to be used to calculate the initial log-likelihood for auto-initalizing
some parameters.
Improve the way OpenMP is specified to compiler
Add comment to Tree::traitValues()
Make beta-related settings optional
Fix: MRCA between the same node is that node
Auto-initialize settings if parameters are omitted
Git: Ignore more variations of output files
CMake: Support Armadillo and LAPACK