Skaffold V2 init does not initialize all manifests.

Consider the sample app https://github.com/yuwenma/skaffold/tree/guestbook-sample-v2 with
- helm charts
- kustomize paths
- raw kubernetes yaml.

The generated skaffold.yaml only initializes the `kustomizePaths` and helm deploy section.

On V1, skaffold init does not support initializing multiple deployers. Creating this as a low priority issue.

Steps to reproduce.
1) checkout above sample
2) Fix the obsolete config. Copy paste below yaml into skaffold.yaml

```
apiVersion: skaffold/v3alpha1
kind: Config
metadata:
name: guestbook

build:
artifacts:
- image: redis-slave
context: redis-slave/
- image: php-redis
context: php-redis
- image: skaffold-helm
context: helm

tagPolicy:
sha256: {}
local:
push: true
manifests:
kustomize:
paths:
- php-redis/config/*.yaml
rawYaml:
- redis-master/*.yaml
kpt:
- redis-slave/
helm:
releases:
- name: skaffold-helm
chartPath: helm/charts
transform:
- name: set-annotations
configMap:
- "author:yuwenma-5"
- name: create-setters
configMap:
- "app:guestbook"
- name: apply-setters
configMap:
- "app:guestbook-yuwen"
validate:
- name: kubeval
deploy:
kpt:
# namespace: default
# name: inventory-90195255
# inventoryID: 3cec9ce7-d9eb-4503-b44c-ffa6ca3a0d49
```

3) run `skaffold init`