command factory with tests
fixed some typo and added some php docs
removed getInstance static method from command classes
changed some new to the command factory
Allow passing of Repository object into XCommand::getInstance() to share the repository's global configs, options and command arguments with the XCommand

This commit removes all CommandFactory logic and functionality
Fully qualified use statements throughout
Unit tests for global configs, options and command args; associated tweaks and fixes
Merge pull request #74 from adamlacoste/feature/global-command-flags

global command flags