Depends on your language of choice. I find that an object oriented approach works well for my projects. I write the core class structure for the shared low-le

Depends on your language of choice. I find that an object oriented approach works well for my projects. I write the core class structure for the shared low-level and common high level functionality. I then create a separate directory for each client. In these, I use inheritance to inject custom sub-classes. In extreme cases, I will replace one module with another.