refactor(util): use structured options for JSON schema cleaning

- Replaced boolean parameters with a `jsonSchemaCleanOptions` struct in `cleanJSONSchema` to improve readability and scalability.
- Updated `CleanJSONSchemaForAntigravity` and related methods to utilize the new options struct.
- Enhanced flexibility for schema transformations with fine-grained control over operations like union flattening, enum type enforcement, and metadata removal.
- Added comprehensive tests to verify correct handling of unions and enum types in schemas.

Closes: #4666