Increase robustness of manifest handling in model generation.

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> The current implementation of `getResolvedManifest` only clears `$ref` fields from schemas within `components/schemas`. While this is sufficient for the current usage in `GenerateFromOpenAPI`, the function is not fully generic. An OpenAPI document can have `$ref`s in other places like `paths`, `parameters`, `responses`, etc. To make this function more robust and reusable, consider extending it to clear `$ref`s 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](https://github.com/meshery/meshkit/pull/924/changes#r2881678676)_

Start at getResolvedManifest and clearSchemaRefs, then trace their use from GenerateFromOpenAPI. Inspect the OpenAPI document's Paths and Components structures to identify the SchemaRef values that need handling; done means references are cleared throughout the document without breaking current model generation.

Written by the indexing model from the issue text.