Added init and update to git submodule command and repository class
Merge pull request #73 from adamlacoste/feature/submodule-update

Added init and update to git submodule command and repository class
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