Setup repo: migrate architecture specs, code stubs, and tasks from alkhub_ts

Copy architecture docs, ADRs, storage domain specs, research, reviews,
and 56 storage architecture tasks from the alkhub_ts monorepo. Adapt for
standalone @alkdev/hub repo structure (src/ not packages/hub/).

Sanitize all sensitive information:
- Replace private IPs (10.0.0.1) with localhost defaults
- Remove internal server hostnames (dev1, ns528096)
- Replace /workspace/ private paths with npm package references
- Remove hardcoded credentials from examples
- Rewrite infrastructure.md without private network details

Add Deno project scaffolding: deno.json (pinned deps), .gitignore,
AGENTS.md, entry point. Migrate existing code stubs (crypto, config
types, logger) with updated import paths.

tasks/sync/update-secondary-docs.md

@@ -0,0 +1,64 @@
+---
+id: update-secondary-docs
+name: Update hub-architecture, hub-config, hub-startup, spoke-runner, ADR-013
+status: completed
+depends_on: [update-call-graph-and-operations-docs, update-pubsub-doc]
+scope: moderate
+risk: low
+impact: component
+level: implementation
+---
+
+## Description
+
+Update the secondary architecture docs that reference the old `packages/core/` paths and pre-extraction status. These docs don't need rewrites — just path and status reference updates.
+
+### hub-architecture.md
+- Component table: Operations row `core/operations/` → `@alkdev/operations`
+- PubSub row: `core/pubsub/` → `@alkdev/pubsub`
+- Call protocol row: `core/` → `@alkdev/operations` (see call-graph.md)
+- WebSocket adapter: "pending" → "available in `@alkdev/pubsub`"
+
+### hub-config.md
+- `createRedisEventTarget` example: add `prefix: "alk:events:"` parameter
+- Update any references to `PendingRequestMap` location
+
+### hub-startup.md
+- Note that PendingRequestMap and CallHandler come from `@alkdev/operations`
+- PubSub setup references `@alkdev/pubsub` with `prefix` option
+
+### spoke-runner.md
+- WebSocket EventTarget: `@alkdev/pubsub/event-target-websocket-client`
+- PendingRequestMap: `@alkdev/operations`
+- Scanner: `@alkdev/operations` with `ScannerFS` Deno adapter (show example)
+- SchemaAdapters: `@alkdev/operations/from-typemap`
+- `FromSchema()` / `FromOpenAPI()`: `@alkdev/operations/from-schema` / `@alkdev/operations/from-openapi`
+
+### ADR-013 (schema-system-integration)
+- Update `packages/core/operations/scanner.ts` → `@alkdev/operations/scanner`
+- Update `packages/core/operations/from_schema.ts` → `@alkdev/operations/from_schema`
+- Update `packages/core/operations/from_openapi.ts` → `@alkdev/operations/from_openapi`
+- Update scanner enhancement task to reference `SchemaAdapter` pattern from `@alkdev/operations/from-typemap`
+
+### mcp-server.md
+- No significant changes needed (MCP server is hub-level, references to MCP client are now via `@alkdev/operations/from-mcp`)
+
+### agent-sessions.md
+- Update `FromOpenAPI` reference to `@alkdev/operations/from-openapi`
+
+### coordination.md
+- Update `FromOpenAPI` reference to `@alkdev/operations/from-openapi`
+
+## Acceptance Criteria
+
+- [ ] hub-architecture.md component table references external packages
+- [ ] hub-config.md Redis ET example includes prefix
+- [ ] hub-startup.md references `@alkdev/operations` for call protocol
+- [ ] spoke-runner.md references `@alkdev/pubsub` and `@alkdev/operations` throughout
+- [ ] ADR-013 paths updated to `@alkdev/operations/*`
+- [ ] No references to `packages/core/operations/` or `packages/core/pubsub/` remain in any secondary doc
+- [ ] No file says "Not started" for WebSocket EventTarget or Call Protocol
+
+## References
+
+- docs/reviews/core-library-extraction-sync-2026-05-18.md (Section 2.8–2.12)