refactor: split monolithic integration test into 7 focused files

[shinpr]

Summary

• Split rag-server.integration.test.ts (1285 lines, 14 describe blocks) into 7 domain-focused test files
• Each file is fully self-contained with its own beforeAll/afterAll setup and teardown
• No test logic changes — all 38 integration tests preserved as-is

New file structure

File	Tests	Scope
rag-server.protocol.integration.test.ts	5	AC-001 MCP protocol + AC-005 basic errors
rag-server.embedding.integration.test.ts	5	AC-003 vector embedding generation
rag-server.search.integration.test.ts	5	AC-004 vector search
rag-server.files.integration.test.ts	9	AC-006 format support + AC-007 file management
rag-server.ingest.integration.test.ts	4	AC-008 re-ingestion + AC-009 error handling
rag-server.delete.integration.test.ts	4	AC-010 file deletion
rag-server.metadata.integration.test.ts	6	File title extraction + meta JSON sidecar

Why this split is safe

• No vi.mock usage in any file (compatible with isolate: false)
• Each describe block already had independent RAGServer instances — no cross-section state dependencies
• Test count verified: 38 before, 38 after

Test plan

• pnpm run check:all passes (509 tests, lint, format, build, unused exports, circular deps)
• Test count preserved (38 integration tests across 7 files)
• CI passes

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