FEAT-611: Refactor filtrage API avec librairie dédiée

📃 TICKET NOTION 📃

• Added missing docs for the filter, sort, limit, and skip filtering. Improved prettier so it actually checks for the md files in website folder

• Refactor filtering API to use api-query-params middleware

Replace custom query parsing with standardized api-query-params library for improved security and maintainability. Update all controllers to use the new query parser middleware and enhance soft delete functionality.

• Replace parseQueryParams and parseMongoFilter with queryParserMiddleware
• Update controller methods to use standardized mongoQueryParams
• Add comprehensive test coverage with new mocking utilities
• Improve soft delete flag naming from searchAlsoInDeletedElements to __showDeleted
• Add proper TypeScript module declarations for Express Request types
• Enhance Jest configuration with ESM support and path mapping