Fixes Issue #147 - Add command-line overrides

Fixes #147

I had to split up the configure method on PluginBase into configure and initialize.  Initialize is now called in the PluginManager constructor and then after command line args are parsed, a new method is called on PluginManager which calls configure in each of the plugins. Without splitting this up, config values could be used in the configure method to populate member variables before they were overridden (i.e. plugins.blockdevice.linux).