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refactor server.go to simplify the invokes to kubeFlags and KubeConfiguration

**What this PR does / why we need it**:
Since kubeFlags and KubeletConfiguration have been fields of KubeletServer, we just need to pass the reference of KubeletServer to the following functions. This will simplify the migrations of flags such as BootstrapCheckpointPath and others, as we don't have to specify from which object the migrated field comes.

**Which issue(s) this PR fixes** *(optional, in `fixes #<issue number>(, fixes #<issue_number>, ...)` format, will close the issue(s) when PR gets merged)*:
Fixes #

**Special notes for your reviewer**:
@mtaufen 

**Release note**:

```release-note
NONE
```