chore(deps): mitigate security findings with verified upgrades

[JWThewes]

Resolve the 14 open Dependabot findings reviewed on September 11, plus both open CodeQL findings. Also patch the Nano ID issue found by a fresh npm audit. Each dependency was checked separately before the next upgrade; the backend and frontend Vitest sets were tested separately with their internal versions aligned.

AgentCore installs from a separate manifest. Pin the affected packages there too, so its image source hash and Docker dependency layer change when this is deployed. Remove the SSM parameter path from the realtime-secret error and isolate the release test helper from its fixed shell probe, with regression tests for both CodeQL findings.

Dependency risk

Upgrade	Regression risk	Individual compatibility evidence
js-yaml 4.3.1 → 4.3.2	Medium: new 100-source YAML merge limit	71 parsing/seeding tests; normal aliases and empty-merge budget regression
brace-expansion 2.1.2 → 2.1.4	Low: extreme expansions are bounded	CommonJS API, padded ranges, character budget, ZIP export
brace-expansion 5.0.7 → 5.0.9	Low: drops Node 18; project uses 22/24	Named API and separate expansion/ZIP checks
Hono 4.13.0 → 4.13.5	Low: stricter query/form handling	82 MCP tests, normal/adversarial queries and forms
qs 6.15.3 → 6.16.0	Low: strict comma-array limit behavior	Both advisory regressions, nested round trips, real MCP Express HTTP form request
Nano ID 3.3.16 → 3.3.18, root and frontend	Low	ESM, CommonJS, browser and async browser checks in each tree; frontend build
Backend Vitest + coverage 4.1.10 → 4.1.11	Low: filesystem allowlist/concurrency backport	1,516 tests with coverage; exact peers validated
Frontend Vitest 4.1.9 → 4.1.11	Low	540 tests and production build

The full compatibility and risk report lists every changed package, including each internal Vitest dependency, all alert IDs, upstream evidence, and residual risks. Other lockfile versions are unchanged. AgentCore's other existing ranges still float: medium residual rebuild risk, checked with a separate production installation, audit, and HTTP/MCP smoke test.

Dependabot PR review

• Incorporates the qs fix from build(deps): bump qs from 6.15.3 to 6.16.0 in the security group across 1 directory #425, independently tested here.
• build(deps): bump @vitest/mocker from 4.1.9 to 5.0.0 in /frontend in the security group across 0 directory #448's diff upgrades frontend Vitest to 5.0.0, despite its mocker-only title. Existing CI is green, but that major has broader mock/configuration/assertion changes. Use the tested 4.1.11 security backport here. The bot PRs remain open.

Validation

• Full backend on Node 22.22.2: 158 files / 2,837 tests passed, including integration tests.
• Shared/agent runtime coverage on Node 24.18.0: 94 files / 1,516 tests passed.
• Frontend on Node 24.18.0: 77 files / 540 tests passed; production build passed.
• Release tooling and security regression suite: 63 tests passed.
• All Lambda workspace builds passed; 37 ESM bundle entry points imported in fresh Node 24 processes.
• Standalone AgentCore: exact security pins verified; HTTP health, YAML parsing, MCP initialization and 20-tool discovery passed.
• Full npm audits, including dev dependencies: 0 vulnerabilities in root, frontend, Yjs, and Cognito lockfiles; standalone AgentCore production audit also 0.
• Clean installs, complete dependency-tree checks, formatter, lint, changed-file secretlint, and AWS SDK alignment passed. Existing lint/Smithy and frontend chunk-size warnings remain.

No live AWS deployment or full container image build was performed. Default-branch security alerts remain open until merge and rescanning. GitHub validation also passed for commit ee7b6419b6ae26300541e0af38deef6d3f428d36.

GitHub validation — passed

• Backend and release tests on Linux Node 22 and 24
• Frontend tests and production build
• Lint, formatting, and SDK alignment
• CodeQL Actions and JavaScript/TypeScript analyses: both succeeded with zero findings; no open code-scanning alerts on refs/pull/456/head.

The linked branch validation runs all used the PR head commit above. All PR-triggered checks also passed, including backend tests on Node 22 and 24, frontend build, lint, and CodeQL.

[jeromevdl]

do we want to keep that in the repo?

[jeromevdl]

do we need to keep this too ?

[jeromevdl]

clean, but there are 2 files I'm not sure we should keep?!

[JWThewes]

I'll remove them

[JWThewes]

Both files deleted