cAdvisor uses Kustomize to manage kubernetes yaml files. See the Kustomize readme for installation instructions, and for a description of how it works.
From the cadvisor/ directory, to generate the base daemonset:
kustomize build deploy/kubernetes/base
To apply the base daemonset to your cluster:
kustomize build deploy/kubernetes/base | kubectl apply -f -
To generate the daemonset with example patches applied:
kustomize build deploy/kubernetes/overlays/examples
To apply the daemonset to your cluster with example patches applied:
kustomize build deploy/kubernetes/overlays/examples | kubectl apply -f -
On your own fork of cAdvisor, create your own overlay directoy with your patches. Copy patches from the example folder if you intend to use them, but don't modify the originals. Commit your changes in your local branch, and use git to manage them the same way you would any other piece of code.
To run the daemonset with your patches applied:
kustomize build deploy/kubernetes/overlays/<my_custom_overlays> | kubectl apply -f -
To get changes made to the upstream cAdvisor daemonset, simply rebase your fork of cAdvisor on top of upstream. Since you didn't make changes to the originals, you won't have any conflicts.