[Refactor/Chore] API Machinery: Migrate API endpoints to layered application services

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Description

Migrate Dify API endpoints toward layered application services, using #39822 as the initial reference implementation. The goal is to make API dependencies, business boundaries, database access, and side effects explicit while preserving existing behavior unless an API contract change is intentionally approved. This is an umbrella issue for the complete API Machinery migration. Individual controller/resource families can be claimed and implemented through separate PRs.

Motivation

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Additional Context

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