refactor: domain-scoped src/ folder structure

[bntvllnt]

Summary

• Restructures flat src/ (8 files, server.ts at 458 LOC) into domain-scoped folders
• src/tools/ — registration, hooks, helpers (query/mutation/action)
• src/resources/ — registration, helpers (resource)
• src/pagination/ — cursor HMAC, handler overrides, config validation
• src/server.ts reduced from 458 to ~130 LOC (thin orchestrator)
• Zero public API changes — DTS output identical (4.90 KB)

Structure

src/
├── server.ts          ~130 LOC (thin orchestrator)
├── auth.ts             47  (unchanged)
├── validators.ts      126  (unchanged)
├── types.ts           shared types + re-exports
├── tools/
│   ├── register.ts    tool registration + hooks
│   ├── helpers.ts     query(), mutation(), action()
│   └── types.ts       ToolDef, CallContext, etc.
├── resources/
│   ├── register.ts    resource registration
│   ├── helpers.ts     resource()
│   └── types.ts       ResourceDef
└── pagination/
    ├── cursor.ts      HMAC encode/decode
    ├── handlers.ts    handler overrides
    ├── context.ts     config validation
    └── types.ts       PaginationConfig, ToolSummary, ToolPage

Test plan

• 103 tests passing (all existing tests, updated imports)
• 100% line/statement/function coverage
• Typecheck clean (both tsconfigs)
• Build output identical (ESM + CJS + DTS, 4.90 KB types)
• Lint clean (0 errors)
• Public API surface unchanged