Is this a BUG REPORT or FEATURE REQUEST?:
/kind bug

Lists in API objects can define a named property that should act as a "merge key". The value of that property is expected to be unique for each item in the list. However, gaps in API validation allow some types to be persisted with multiple items in the list sharing the same value for a mergeKey property.

The algorithm used by kubectl apply detects removals from a list based on the specified key, and communicates that removal to the server using a delete directive, specifying only the key. When duplicate items exist, that deletion directive is ambiguous, and the server implementation deletes all items with that key.

Known API types/fields which define a mergeKey but allow duplicate items to be persisted:

PodSpec (affects all workload objects containing a pod template):

• hostAliases (kubectl apply drops all hostAlias entries when removing a duplicate entry from an existing object #91670)
• imagePullSecrets (kubectl apply removes all imagePullSecrets when user attempts to remove duplicate secrets #91629)
• containers[*].env (this issue, Failed to create three way merge patch when container environment variable specified multiple times #86163, Deployment objects using optional envs with the same name are unexpectedly removed during updates - but exist out of the box #93266, Removing a duplicate environment variable from the container spec ends up deleting the environment var entirely #106809, Env variable is missing in container, after cleanup of duplications in deployment #121541, Upgrade StatefulSet, key missing in env #122121)
• containers[*].ports (Container Ports for pods vanishing #86273, Duplicate ports in deployment results in non-deterministic port assignment #93952, Deployment containerPort Duplicate value issue #113246)
• volumes (kubectl apply admits Deployment with duplicate volumes then fails when renaming duplicate #78266)
• containers[*].volumeMounts (Change merge key for VolumeMount to mountPath #35071 changed the merge key from name to mountPath, which was a breaking change, but mountPath is at least required to be unique)

Service

• ports (name+protocol required to be unique on create in Validate if service has duplicate port #47336, but still has issues on update in apiserver allows duplicate service port #59119, No error or warning message when service modified with partially success. #97883, and mergeKey is still only name, xref PATCH merges Services with same port, different protocol #47249)

Original report

===

What happened:
For deployment resource:

A container has defined environment variable with name x that is duplicated (there are two env vars with the same name, the value is also the same).

When you fix the deployment resource descriptor so that environment variable with name x appears only once and push it with kubectl apply, deployment with no environment variable named x is created and therefore no environment variable named x is passed to replica set and pods.

What you expected to happen:
After fixing the deployment, environment variable with name x is defined in the deployment once .

How to reproduce it (as minimally and precisely as possible):

1. create deployment with container with duplicated environment variable
2. kubectl apply it
3. fix deployment removing one of duplicated environment variable definitions
4. kubectl apply it
5. kubectl get deployment/your-deployment -o yaml prints deployment without

Anything else we need to know?:
nope

Environment:

• Kubernetes version (use kubectl version):
  Client Version: version.Info{Major:"1", Minor:"9", GitVersion:"v1.9.1", GitCommit:"3a1c9449a956b6026f075fa3134ff92f7d55f812", GitTreeState:"clean", BuildDate:"2018-01-04T20:00:41Z", GoVersion:"go1.9.2", Compiler:"gc", Platform:"darwin/amd64"} Server Version: version.Info{Major:"1", Minor:"9", GitVersion:"v1.9.1", GitCommit:"3a1c9449a956b6026f075fa3134ff92f7d55f812", GitTreeState:"clean", BuildDate:"2018-01-04T11:40:06Z", GoVersion:"go1.9.2", Compiler:"gc", Platform:"linux/amd64"}
• Cloud provider or hardware configuration: private Kubernetes cluster
• OS (e.g. from /etc/os-release): N/A
• Kernel (e.g. uname -a): N/A
• Install tools: N/A
• Others: N/A