By default operator-sdk generates folder structure as following
root_folder
|- api
|- config
|- |- crd
|- |- default
|- |- manager
|- |- ..
|- controllers
|- hack
some folders have been omitted for brevity.
What I am looking for is how to modify this folder structure and configure operator sdk to honor that folder structure.
So say I want to rename config to cmd, how to achieve this when using operator-sdk
You kind of can't. Some stuff is based on special comments and will mostly work no matter the layout but the further you deviate from the default layout, the more of the scaffolding won't work for you in the future.
That said, you can just do whatever you want and not use OSDK again. The underlying Go libraries (controller-runtime, controller-tools) mostly don't care about layouts and it's your software so you can do whatever.