Here is a list of all documented files with brief descriptions:

demographic_function.h	Contain the demographic function P(t+1) = f(P(T)). By default it is P(t+1) = a + b * P(T) + c * P(T) * P(T), but it is easy to modify, and everythign will follow OK.
genetics.h	Define the class DNA.
human.h	Define the class of individuals without DNA.
humandna.h	Define the class of individuals with DNA and mtDNA.
humanmt.h	Define the class of individuals with mtDNA (no DNA).
population.h	Define the class for population.
simulation.h	Define the class for simulations.
utils.h	Define a set of useful function to manipulate data. Also define the number of bits of the system (32 or 64), which should be detected automatically.