Reimplement configuration files

[chrisbrickhouse]

In #61 we decided to reimplement config files using YAML. This is a tracking task for that goal.

Specs

• Configuration file settings MUST overwrite defaults.
• Command line flags MUST overwrite configuration file settings
• The old method using argparse where flags were specified in a file MUST remain for backwards compatibility
• An external YAML parser SHOULD be used (probably PyYAML)

To do

• Write tests for the "must" specs above
• Implement yaml config
• write tutorial / documentation page