Magento’s file structure becomes muddy waters when its code pools are filled with third party extensions. Developing your own extension or module doesn’t have to feel like hiking in swamp lands. By using symlinks and developing your code outside Magento’s deep file structure, you can separate your code from the mess.
Mediotype developers don’t accomplish this manually, we use Colin Mollenhour’s Modman (Module Manager) (link: https://github.com/colinmollenhour/modman) for coupling/decoupling our extensions and modules.
Modman requires a symlink declaration file and a short deploy command to couple entire code structures to Magento from an external file location. Modman has Git integration, so a ‘modman clone <Git link>’ command will grab your code structure from Git and symlink it to your project in one hack without any flashlights or muddy boots.