Increase robustness of manifest handling in model generation.

[l5io]

The current implementation of getResolvedManifest only clears $ref fields from schemas within components/schemas. While this is sufficient for the current usage in GenerateFromOpenAPI, the function is not fully generic. An OpenAPI document can have $refs in other places like paths, parameters, responses, etc. To make this function more robust and reusable, consider extending it to clear $refs from the entire document. For example, you could iterate through doc.Paths and other parts of doc.Components and call clearSchemaRefs on any SchemaRef found.

Originally posted by @gemini-code-assist[bot] in #924

[welcome]

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