Update $ref references

According to [dos](http://spacetelescope.github.io/understanding-json-schema/structuring.html) This is how `$ref` should be used: 

```json
{
  "$schema": "http://json-schema.org/draft-04/schema#",

  "definitions": {
    "address": {
      "type": "object",
      "properties": {
        "street_address": { "type": "string" },
        "city":           { "type": "string" },
        "state":          { "type": "string" }
      },
      "required": ["street_address", "city", "state"]
    }
  },

  "type": "object",

  "properties": {
    "billing_address": { "$ref": "#/definitions/address" },
    "shipping_address": { "$ref": "#/definitions/address" }
  }
}
```
results to: 

```json
{
  "shipping_address": {
    "street_address": "1600 Pennsylvania Avenue NW",
    "city": "Washington",
    "state": "DC"
  },
  "billing_address": {
    "street_address": "1st Street SE",
    "city": "Washington",
    "state": "DC"
  }
}
```


That is the same for our case.
```yaml
models:
  Pet:
    required:
      - id
      - name
    properties:
      id:
        type: integer
        format: int64
      name:
        type: string
      tag:
        type: string
paths:
  /pets:
    get:
      responses:
        200:
          description: pet response
          schema:
            type: array
            items:
              Pet:
                $ref: '#/models/Pet'
```
That should resolve to:

```yaml
models:
  Pet:
    required:
      - id
      - name
    properties:
      id:
        type: integer
        format: int64
      name:
        type: string
      tag:
        type: string
paths:
  /pets:
    get:
      responses:
        200:
          description: pet response
          schema:
            type: array
            items:
              Pet:
                required:
                  - id
                  - name
                properties:
                  id:
                    type: integer
                    format: int64
                  name:
                    type: string
                  tag:
                    type: string
```yaml

/cc @earth2marsh