Difference between skeleton and main app?

I am just starting out with Slim framework, what are the key differences between https://github.com/slimphp/Slim-Skeleton and https://github.com/slimphp/Slim/tree/3.x/Slim is there anything vital the skeleton app is missing?

No, the other way around. https://github.com/slimphp/Slim is the base framework and https://github.com/slimphp/Slim-Skeleton is a suggestion of how you might configure and setup an app. The Skeleton is an example project that uses Slim and slimphp/Slim is the framework itself.

But if I am using the skeleton app it is still using the framework, or not at all or only slightly?

It is still using it fully.

Many thanks for that.