Update pattern

[nossleinad]

Novelties

• This is a continuation of Root optim #40, i.e. we introduce root_optim! and root_update! here, which are similar to branchlength/nni_update! in style/conceptually
• We enable models-updates, but here we offload to the user and don't implement our own models-updating-algorithm.
• We develop an "update interface" which makes it easy to define how a phylogenetic tree should be updated by mixing and matching between nni/branchlength/root/model_update!

Modifications

• In our metropolis_step interface, we can now transform the current value into a convenient parameter-space, which makes it easies to write clean proposal and log_prior definitions.

Arguably sketchy stuff

• The names for the transformations in metropolis_step, I call tr and invtr which maybe aren't top names.
• When we want to sample the root K times per MCMC iteration with StandardUpdate, instead of putting root=K in the StandardUpdate-constructor, we let our ConcreteRootSample <: RootSample have Base.length(::ConcreteRootSample) = K. This is a bit hacky and weird but it's because we only need to call felsenstein_roundtrip! once and not K times to do this.
• If we want to save the models-trace during metropolis_sample, it's currently stored in a Vector{Any}. We can compress the stuff that's stored in that vector by collapse_models, but Vector{Any} is probably quite bad for performance.