You may start from WP Kirk repo as a boilerplate to create a WP Bones WordPress plugin.
I love Laravel
First to all, this framework and the boilerplate plugin are inspired to Laravel framework. Also, you will find a bones php shell executable like Laravel artisan.
After cloning the repo, you can:
$ php bones
$ php bones namespace MyPluginName
The last command is very important. You can change the namespace in anytime. However, I suggest you to make this only the first time, when the plugin is inactive.
After changing of the namespace, you can start to develop you plugin. Your namespace will be MyPluginName.