`kubectl apply` (client-side) removes all entries when attempting to remove a single duplicated entry in a persisted object

**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` (#91670)
* `imagePullSecrets` (https://github.com/kubernetes/kubernetes/issues/91629)
* `containers[*].env` (this issue, https://github.com/kubernetes/kubernetes/issues/86163, https://github.com/kubernetes/kubernetes/issues/93266, https://github.com/kubernetes/kubernetes/issues/106809, https://github.com/kubernetes/kubernetes/issues/121541, https://github.com/kubernetes/kubernetes/issues/122121)
* `containers[*].ports` (#86273, https://github.com/kubernetes/kubernetes/issues/93952, https://github.com/kubernetes/kubernetes/issues/113246, https://github.com/kubernetes/kubernetes/issues/134470)
* `volumes` (https://github.com/kubernetes/kubernetes/issues/78266)
* ~~`containers[*].volumeMounts`~~ (https://github.com/kubernetes/kubernetes/pull/35071 changed the merge key from name to mountPath, which was [a breaking change](https://github.com/kubernetes/kubernetes/issues/36024#issuecomment-261169033), but mountPath is at least required to be unique)

Service
* `ports` (name+protocol required to be unique on create in https://github.com/kubernetes/kubernetes/pull/47336, but still has issues on update in https://github.com/kubernetes/kubernetes/issues/59119, #97883, and mergeKey is still only name, xref https://github.com/kubernetes/kubernetes/issues/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
1. `kubectl apply` it
1. fix deployment removing one of duplicated environment variable definitions
1. `kubectl apply` it
1. `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

Start with the client-side kubectl apply list-merge logic and the server handling of delete directives described in the issue. Reproduce the deployment case with duplicated environment variables, then trace how removing one duplicate is represented and applied. Done means applying the corrected deployment preserves one environment variable with that name instead of removing all matching entries.

Written by the indexing model from the issue text.