Add Log class

Instead of writing to std::cout directly, use the log()
function, which is defined when you include "Log.h".
You do not need to create a Log class, just use log().

For example, to write a plain message to standard output:

  log() << "This is a message.\n";
  log(Message) << "This does the same as above.\n";

To write a warning or error to standard error:

  log(Warning) << "This is a warning.\n";
  log(Error) << "This is an error.\n";

You can specify the output stream to write to.
For example, to write to a file named "log.txt":

  std::ofstream out("log.txt");
  log(out) << "This is a message.\n";
  log(Message, out) << "This does the same as above.\n";
  log(Warning, out) << "This is a warning.\n";
  log(Error, out) << "This is an error.\n";
  out.close();
Modify Makefile to handle the Log class
Turn on additional compiler warnings
Use log() when writing messages or errors

- There are still many places that don't use log(), but the most
  common places do. Eventually, everything should use log().

- A general message about BAMM was added to the screen output.

- Other output messages, including the MCMC parameter values were
  cleaned up and aligned better.

- The check to see if output files can be overwritten was moved to
  the Settings class.
Merge branch 'logger'

Conflicts:
	src/TraitMCMC.cpp