[Kinkytech]

closes #583
closes #612
closes #613
closes #582

Note: #582 (unit tests for timeout middleware) is not included. tests/unit/middleware/timeout.test.ts already exists at exactly the path the issue asks for and covers default timeout, per-route override, and the timeout response (408, not the 504 the issue's acceptance criteria names, matching what registerRequestTimeout actually sends). 4/4 passing, confirmed, not claiming it here.

Infra fix (required before #612/#613 could even boot a server)

Same repo-wide breakage already reported in full in #689: every E2E test crashes before buildApp() finishes, confirmed on a clean clone of main. Since #612 and #613 both ask for new E2E coverage, fixed it here too rather than write tests against a server that cannot boot. Full detail is in the first commit's message and mirrors #689: the logger.ts/config/index.ts circular import, the Fastify logger vs loggerInstance option, process-webhook-retries.ts's two concatenated implementations, dead NestJS-style scaffold code bolted onto several real files (course.service.ts, credential.controller.ts, credential.service.ts, reward.controller.ts, plus three fully-dead files and the whole src/modules/quizes/ directory), duplicate route registrations in course.routes.ts/admin-course.routes.ts, and a ReferenceError in webhook-dispatcher.ts's sendWebhook().

New bug found while writing #612's content-management tests: admin-course.routes.ts's POST .../modules/:moduleId/content route had a Fastify-level JSON Schema (body: { content: string, contentType, videoUrl }) that doesn't match course.types.ts's createContentSchema at all, a Zod discriminated union keyed on a required type field, with content as an object shaped per type (text/video/quiz/exercise). Fastify validates the route's own JSON Schema before the Zod preHandler ever runs, so any request shaped for the real schema was rejected with FST_ERR_VALIDATION, this endpoint could not succeed with any input. Rewrote the route schema to match createContentSchema's actual shape.

What's added

• tests/unit/middleware/deprecation.test.ts (Add unit tests for deprecation middleware #583): deprecationHeader() is a preHandler factory attaching RFC 8594 Deprecation/Sunset/Link headers. It isn't currently attached to any route (confirmed via a repo-wide search), so there's no endpoint-matching logic beyond the factory's own header construction to test; covered that: the Deprecation: true header, the Sunset header as a valid RFC 7231 HTTP-date, the Link header's successor-version computation, and that all three are set independent of request contents.
• tests/e2e/admin-courses.test.ts (Add E2E tests for admin course management #612): course CRUD, module management (create/update/delete), content management (create/list/delete, the bug above was found and fixed writing these), and course publishing (publish-check correctly reporting a module-less course as not ready, and publish itself rejecting that same course).
• tests/e2e/admin-badges.test.ts (Add E2E tests for admin badge management #613): badge CRUD. For "assignment" and "progress tracking": there's no admin assignment endpoint; badges are evaluated and auto-awarded against a user's real activity on every call to GET /users/me/badges (badge.service.ts's evaluateUserBadges). Covered that end to end: seeding real enrollment data against an admin-created badge's criteria, confirming its progress before it's earned, and confirming it gets auto-awarded once the criteria are met.

30 tests, all passing. Also confirmed courses.test.ts, credentials.test.ts, rewards.test.ts, and quizzes.test.ts all still pass (no regressions from the scaffold cleanup).

Disclosure: course-modules.test.ts has 3 pre-existing failures unrelated to anything touched here, confirmed present before this PR too.

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