Bundling Creates Redundant Schema Objects for `$defs`

Describe the bug
Bundling a multi-file OpenAPI spec using $defs creates redundant schema objects in the bundled file.

To Reproduce

1. Create a multi-file OpenAPI spec that contains a schema object with $defs:

main.yaml

openapi: 3.1.0

info:
  title: API
  version: v1

servers:
  - url: https://domain.com

components: {}

paths:
  /test:
    get:
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: './schemas.yaml#/MyObject'

schemas.yaml

MyObject:
  type: object
  properties:
    key:
      $ref: '#/MyObject/$defs/anotherObject'
  $defs:
    anotherObject:
      type: object
      properties:
        anotherKey:
          type: string

.redocly.yaml

apis:
  example:
    root: main.yaml

2. run openapi bundle example -o bundled.yaml

See that the bundled file has a redundant anotherObject schema that is being used in place of MyObject/$defs/anotherObject

bundled.yaml

openapi: 3.1.0
info:
  title: API
  version: v1
servers:
  - url: https://domain.com
components:
  schemas:
    anotherObject:
      type: object
      properties:
        anotherKey:
          type: string
    MyObject:
      type: object
      properties:
        key:
          $ref: '#/components/schemas/anotherObject'
      $defs:
        anotherObject:
          type: object
          properties:
            anotherKey:
              type: string
paths:
  /test:
    get:
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/MyObject'

Expected behavior
The bundled file should use the existing definition instead of creating a duplicate schema object.

Redocly Version(s)
1.0.0-beta.113

Start by reproducing the issue with main.yaml, schemas.yaml, and .redocly.yaml, then run openapi bundle example -o bundled.yaml and compare the generated schemas with the expected structure. Trace the bundling path that handles $defs; done means the bundle reuses MyObject/$defs/anotherObject instead of creating a duplicate top-level schema.