fix(deps): resolve all medium-severity Dependabot security alerts

[KIvanow]

Summary

Follow-up to #364: fixes all open medium-severity Dependabot alerts that are fixable without breaking runtime consumers (12 of 13 alerts across 5 packages; the one exception is dismissed with justification, see below). Same approach as #364 — root pnpm.overrides, one commit per package, each verified by building the affected app(s) and running their test suites.

Vulnerabilities fixed:

1. CVE-2026-69207 — hono < 4.12.34: ReDoS in CORS middleware via Access-Control-Request-Headers → 4.13.1
2. CVE-2026-59896 — hono < 4.12.27: hono/jsx context not isolated per request (cross-request data disclosure) → 4.13.1
3. CVE-2026-59895 — hono < 4.12.27: server-side XSS via JSX escaping bypass in cx() → 4.13.1
4. CVE-2026-59897 — hono < 4.12.27: API Gateway v1 adapter drops distinct repeated request header values → 4.13.1
5. CVE-2026-49978 — dompurify ≤ 3.4.6: IN_PLACE bypass via attached shadow root inside <template>.content → 3.4.13
6. CVE-2026-49458 — dompurify ≤ 3.4.5: cross-realm IN_PLACE sanitization leaves executable markup → 3.4.13
7. CVE-2026-49459 — dompurify ≤ 3.4.5: IN_PLACE preserves attributes of clobbered root element (XSS) → 3.4.13
8. CVE-2026-65902 — dompurify < 3.4.7: hook mutation permanently pollutes default allowlists → 3.4.13
9. CVE-2026-65898 — dompurify ≤ 3.4.10: permanent ALLOWED_ATTR pollution via setConfig() (incomplete-fix follow-up) → 3.4.13
10. CVE-2026-59952 — valibot ≤ 1.4.1: record() issue paths make flatten() throw for inherited Object property names (DoS) → 1.4.2
11. GHSA-frvp-7c67-39w9 — @hono/node-server < 2.0.5: path traversal in serve-static on Windows via encoded backslash → 2.1.0
12. CVE-2026-54285 — @opentelemetry/core < 2.8.0: unbounded memory allocation in W3C Baggage propagation → 2.9.0 (also dedupes the orphaned 1.30.1/2.2.0/2.6.1 copies to one resolution)

Three dompurify low alerts (#253, #255, #256) close as a side effect of the 3.4.13 bump.

Intentionally not fixed — file-type ASF-parser infinite loop (CVE-2026-31808, alert #45): the vulnerable file-type@16.5.4 exists only inside ibm-cloud-sdk-core (pulled via @ibm-cloud/watsonx-ai ← @langchain/community), a code path this app never exercises. The patched 21.x line is ESM-only and verifiably breaks the SDK's CJS FileType.fromBuffer call (getContentType(Buffer) throws TypeError — reproduced locally before reverting). Alert dismissed as "vulnerable code is not actually used"; revisit if ibm-cloud-sdk-core updates its file-type dependency.

Changes

• Raised/added pnpm.overrides in the root package.json: hono >=4.12.34, dompurify >=3.4.11, valibot >=1.4.2 <2, @hono/node-server >=2.0.5 <3, @opentelemetry/core >=2.8.0 <3
• Regenerated pnpm-lock.yaml (per-package commits; each diff scoped to that package's chain)
• Bumped packages/agent-memory devDependency @opentelemetry/sdk-trace-base ^1.30.1 → ^2.9.0: the core 2.x override broke the 1.x SDK's getEnv() import, failing the span tests (caught by Bugbot). The tests already use the 2.x spanProcessors API, so no test changes were needed; this also removes the last @opentelemetry 1.x entries from the lockfile.

Verification (per commit + final sweep): pnpm install --frozen-lockfile passes; full workspace build (13 turbo tasks) green; apps/web suite fully green (45 files, 309 tests); apps/api suite green (~2,616 tests) except the known pre-existing environment-dependent failure (license.service.spec reads a real license key from the local env; fails identically on unmodified master). Note the @hono/node-server 1.x→2.x major: peer range stays hono ^4 and the MCP SDK consumer's suites pass unchanged. packages/agent-memory suite fully green after the sdk-trace-base bump (28 files, 207 tests).

Checklist

• Unit / integration tests added — N/A, dependency version bumps only; existing suites pass
• Docs added / updated — N/A
• Roborev review passed — run roborev review --branch or /roborev-review-branch in Claude Code (internal)
• Competitive analysis done / discussed (internal)
• Blog post about it discussed (internal)

---

Note

Medium Risk
Medium risk from the @hono/node-server major bump and workspace-wide OTel 2.x consolidation; changes affect MCP SDK, Prisma dev tooling, and telemetry paths, though described as test-verified.

Overview
Raises minimum resolved versions through root pnpm.overrides and regenerates pnpm-lock.yaml to close multiple medium-severity Dependabot alerts—no application source changes.

Overrides added or tightened: hono (≥4.12.34), dompurify (≥3.4.11), valibot (≥1.4.2), @hono/node-server (≥2.0.5, major from 1.x), and @opentelemetry/core (≥2.8.0). The lockfile resolves hono 4.13.1, dompurify 3.4.13, @hono/node-server 2.1.0, valibot 1.4.2, and consolidates OpenTelemetry core / sdk-trace-base on 2.9.0 (dropping older 1.30.x / 2.2.x copies).

packages/agent-memory: devDependency @opentelemetry/sdk-trace-base moves from ^1.30.1 to ^2.9.0 so span tests align with the unified OTel stack pulled in via LangChain/langsmith and related packages.

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