[Bug]: allOf reference not resolved fully

Start with the OpenAPIV3Parser and ParseOptions behavior shown in the issue, then reproduce the case from the linked repository using the provided OpenAPI 3.0.3 document. Trace why resolveFully(true) leaves the $ref inside Contact's allOf unresolved; done means the referenced SObject schema is expanded while the raw second allOf schema remains intact.

Description

Setting resolveFully(true) does not resolve $ref pointers inside allOf schemas. The $ref remains as a pointer.

This is while Parsing OpenAPI 3.0.x specs. In case it's relevant, the allOf I'm trying to parse contains a $ref AND a raw schema as the 2nd element.

Affected Version

• 2.1.22 (latest)

Steps to Reproduce

Full reproducible example here: https://github.com/julianmclain/swagger-parser-allOf-resolution

Set ParseOptions.setResolve(true) and setResolveFully(true) and parse a spec with a schema using allOf:

String spec = """
    {
      "openapi": "3.0.3",
      "info": { "title": "Test", "version": "1.0" },
      "paths": {},
      "components": {
        "schemas": {
          "SObject": {
            "type": "object",
            "properties": {
              "attributes": { "type": "object" }
            }
          },
          "Contact": {
            "allOf": [
              { "$ref": "#/components/schemas/SObject" },
              {
                "type": "object",
                "properties": {
                  "FirstName": { "type": "string" }
                }
              }
            ]
          }
        }
      }
    }
    """;

ParseOptions options = new ParseOptions();
options.setResolve(true);
options.setResolveFully(true);

SwaggerParseResult result = new OpenAPIV3Parser().readContents(spec, null, options);
Schema<?> contact = result.getOpenAPI().getComponents().getSchemas().get("Contact");

System.out.println(Json.pretty(contact.getAllOf()));

Expected Behavior

The $ref is resolved to the referenced schema content, i.e.

[ {
  "type" : "object",
  "properties" : {
    "attributes" : {
      "type" : "object"
    }
  }
}, {
  "type" : "object",
  "properties" : {
    "FirstName" : {
      "type" : "string"
    }
  }
} ]

Actual Behavior

The reference to "#/components/schemas/SObject"` is unresolved:

[ {
  "$ref" : "#/components/schemas/SObject"
}, {
  "type" : "object",
  "properties" : {
    "FirstName" : {
      "type" : "string"
    }
  }
} ]

Environment

• Java version: 21
• Build tool: Gradle 9.0
• OS: macOS

Additional Context

There were related issues, but they were marked resolved so I'm not sure if they're relevant: #1157, #1161, #1538

Checklist

• I have searched the existing issues and this is not a duplicate.
• I have provided sufficient information for maintainers to reproduce the issue.