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/architecture/storage/add-partial-indexes.md

@@ -0,0 +1,48 @@
+---
+id: add-partial-indexes
+name: Add Partial Indexes and Call Graph Index Improvements
+status: completed
+depends_on: ["add-missing-indexes-identity", "add-missing-indexes-observability", "add-missing-indexes-sessions"]
+scope: narrow
+risk: low
+impact: component
+level: implementation
+---
+
+## Description
+
+Four related index/constraint improvements across different domains:
+
+1. **S02**: Add partial indexes for common access patterns — active API keys (`WHERE revoked_at IS NULL AND enabled = true`), connected spokes (`WHERE status = 'connected'`), non-archived sessions, active tasks (`WHERE status IN ('pending', 'in-progress', 'blocked')`).
+
+2. **S04**: Add `accounts.displayName` index for user search/autocomplete UIs. Without it, user search requires full table scans.
+
+3. **S17**: Add `call_graph_nodes.startedAt` index alongside or instead of `createdAt` for p99 latency analysis queries.
+
+4. **S18**: Add unique constraint on `call_graph_edges(sourceId, targetId, edgeType)` to prevent duplicate edges from retries/reconnections.
+
+## Acceptance Criteria
+
+- [ ] Partial indexes defined in `table-reference.md` for: active API keys, connected spokes, non-archived sessions, active tasks
+- [ ] `displayName` index added to accounts table in `identity.md` and `table-reference.md`
+- [ ] `startedAt` index added to call_graph_nodes in `call-graph.md` and `table-reference.md`
+- [ ] Unique constraint on `(sourceId, targetId, edgeType)` added to call_graph_edges in `call-graph.md` and `table-reference.md`
+- [ ] All indexes documented with WHERE clauses/purpose in per-domain docs
+
+## References
+
+- docs/reviews/storage-architecture-review-2026-04-21.md#S02
+- docs/reviews/storage-architecture-review-2026-04-21.md#S04
+- docs/reviews/storage-architecture-review-2026-04-21.md#S17
+- docs/reviews/storage-architecture-review-2026-04-21.md#S18
+- docs/architecture/storage/table-reference.md
+- docs/architecture/storage/identity.md
+- docs/architecture/storage/call-graph.md
+
+## Notes
+
+> To be filled by implementation agent
+
+## Summary
+
+> To be filled on completion