[Bug] Selective API operation extraction filter does not filter paths in specification.yaml

Start with the apiops extract entry point and the filter configuration at configuration/extractor.config.yaml. Compare how the operations allow-list is applied to artifacts/apis/api1/operations/ versus artifacts/apis/api1/specification.yaml. Done means the specification contains only the selected operation paths while excluded operation artifacts remain absent.

Command that triggered the bug

apiops extract

Expected behavior

When an API is configured with an operations allow-list, the generated specification.yaml should contain only those selected operations.

For example:

apis:
  - api1:
      operations:
        - create-resources

If the api1 API contains create-resources and test, only create-resources should appear in: specification.yaml



### Actual behavior

The extractor correctly filters the individual operation artifacts. Only the selected operation is generated under:

artifacts/apis/api1/operations/

However, artifacts/apis/api1/specification.yaml still contains the other operations path.

As a result, publishing the extracted artifacts can create the excluded operation in the target APIM instance, even though it was not listed in the extractor filter.

This is the same behavior described in for the older apiops [Azure/apiops#854](https://github.com/Azure/apiops/issues/854).

### apiops CLI version

1.0.3

### Environment details

APIOps CLI package: @azure-tools/apiops-cli
APIOps CLI version: 1.0.3
Node.js: 22.x or later
Package installation: npm ci
Command: apiops extract
Filter option: --filter configuration/extractor.config.yaml

### CI/CD environment

Azure DevOps

### Is this bug blocking you?

Yes