Start to implement Metropolis coupled MCMC
Copy some MCMC methods to MetropolisCoupledMCMC
Changes related to previous commit
First working implementation of Metropolis MCMC
Print out the temperature of each chain
Fix chain swap acceptance probability equation

In addition,
  - Print out the swap acceptance rate to screen and to mcmc_out.txt
  - Add MCMCMC parameters to the Settings class:
    - numberOfChains
    - deltaT
    - swapPeriod
Start to add MC3-specific output
Specify C++11 in CMakeLists.txt
Re-format MC3 output

The default file mc3_out.txt is created, which contains the rank of
each chain and information about that chain per line.
Output chain swap information
Add a missing include
Remove dependency on C++11
Give MCMC output method the correct generation
Add acceptanceResetFreq option

This option specifies the number of generations after which to reset
each chain model's accept/reject counts.