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-packages-and-dependencies.md

@@ -0,0 +1,38 @@
+---
+id: update-packages-and-dependencies
+name: Update packages.md Dependency Structure
+status: completed
+depends_on: []
+scope: narrow
+risk: low
+impact: component
+level: implementation
+---
+
+## Description
+
+Update `docs/architecture/packages.md` to reflect the new dependency structure: `@alkhub/core` is removed, hub and spoke import directly from `@alkdev/*` npm packages.
+
+### Key changes
+
+1. Remove `@alkhub/core` section entirely
+2. Add sections for the 3 external `@alkdev/*` packages with their exports
+3. Update `@alkhub/hub` dependencies: add `@alkdev/operations`, `@alkdev/pubsub`, `@alkdev/taskgraph`; remove `@repeaterjs/repeater` (inlined in pubsub)
+4. Update `@alkhub/spoke` dependencies: add `@alkdev/operations`, `@alkdev/pubsub`
+5. Update dependency direction: `spoke → @alkdev/operations, @alkdev/pubsub`, `hub → @alkdev/operations, @alkdev/pubsub, @alkdev/taskgraph`
+6. Update rules: replace "core is transport-agnostic" with "packages should be transport-agnostic"
+7. Note that `ioredis` is now an optional peer dep of `@alkdev/pubsub` (only if Redis ET is used), not a direct dep of hub
+8. Note that `@modelcontextprotocol/sdk` is an optional peer dep of `@alkdev/operations` (only if MCP adapter is used)
+
+## Acceptance Criteria
+
+- [ ] `@alkhub/core` section is removed
+- [ ] 3 external `@alkdev/*` package sections are documented with exports
+- [ ] Hub and spoke dependency lists are updated
+- [ ] Dependency direction diagram is updated
+- [ ] Rules section reflects new structure (no core package)
+- [ ] Storage location decision section still applies (unchanged)
+
+## References
+
+- docs/reviews/core-library-extraction-sync-2026-05-18.md (Section 2.3)