We use a combination of Paket and Paket.Unity3D in our projects for internal dependency management. There is also a wrapper called Wooget for both, but since we don't maintain it anymore, i will not cover it.
We always need 2 steps to update depenencies:
- Paket to Install all defined depenency for your project.
- Paket.Unity3D to add them to the Unity Project.
The Documentation is based on the recommended project structure.