Fixing plugin's AppController bake generation

It was being baked into the top folder instead of src
Initial code to modify composer's autoloader after baking a plugin
Fixing an error when calling composer and adding doc block
Moving a pice of code to a better home
Modified the rest of the shell tasks to account for the new plugin folder structure
Fixing plugin paths in all bake tasks
Fixed typo
Fixed another typo
Moving plugin path generation to where it belongs
Added missing autoloader for plugin test cases
Merge pull request #3732 from cakephp/3.0-plugin-bake

3.0 plugin bake