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did you make any changes on the resource? `refresh` will simply take the currently managed resources and update the stack

Yes. I do the following steps
1. Init a new pulumi stack
2. Create a nginx deployment to k8s with replicas=1
3. Pulumi up 
4. Edit the k8s cluster: change replicas=2 by kubectl edit
5. Pulumi refresh. It shows there is an update on nginx deployment. 
1. When i try to use pulumi up(replica=1 in code), it shows there is no change. But if i modify the code, set replica=2, it shows there is an update.. 

I see there are two fields named 'input' in stack json file. What's the different? And the code will be compared with the second input field to get changes

This is the same issue as <https://github.com/pulumi/pulumi-kubernetes/issues/694>