Deleted simulations .R files in the R directory

These now live in not-package/simulations/simulation_functions.R

Note that I renamed simulation_equations.R to simulation_functions.R
Cleaned up names of histogram pdf files

also fixed a bug in MCMC_atable
Fixed allele CI overlap stuff

I deleted the MCMC_atable function as it didn't seem to work and I did it using aggregate. See the new code in 03_maketables.

Also minor fixes to other files.