security: Dependabot high/critical vulnerability remediation (umbrella)

[vybe]

Summary

116 total Dependabot alerts are open, including 1 critical and 33 high severity vulnerabilities across the frontend and MCP server dependencies. This umbrella tracks remediation of all critical and high severity items as a coordinated effort.

Context

Dependabot has flagged a wide surface of vulnerabilities in the `src/frontend/` and `src/mcp-server/` dependency trees. The most impactful packages — `happy-dom`, `@modelcontextprotocol/sdk`, `hono`, `axios`, and `vite` — affect runtime paths (JWT auth, HTTP client, dev server, MCP session isolation). These should be resolved before any public-facing release.

Affected Packages (Critical + High)

Severity	Package	Key CVE Summary
CRITICAL	happy-dom	VM context escape → RCE (#83)
HIGH	@modelcontextprotocol/sdk	Cross-client data leak, ReDoS, session auth bypass (#2, #5, #16, #17)
HIGH	hono	JWT algorithm confusion, JWK bypass, file-read via serveStatic (#6, #7, #27, #28)
HIGH	axios	Prototype pollution, header injection (#93, #94, #95, #96)
HIGH	vite	Arbitrary file read via dev server (#55)
HIGH	fast-uri	Host confusion + path traversal via percent-encoding (#113, #114, #121, #122)
HIGH	path-to-regexp	ReDoS via sequential quantifiers (#51, #53)
HIGH	picomatch	ReDoS via extglob quantifiers (#48, #49)
HIGH	undici	WebSocket memory/parser overflows (#41, #43, #45)
HIGH	express-rate-limit	IPv4-mapped IPv6 bypass per-client limits (#35, #36)
HIGH	@hono/node-server	Authorization bypass for protected static routes (#33, #34)
HIGH	rollup	Arbitrary file write via path traversal (#26)
HIGH	koa	Host header injection via ctx.hostname (#25)
HIGH	happy-dom	Cookie credential leak + ECMAScript compiler injection (#84, #85)

Acceptance Criteria

• All 1 critical alerts resolved (happy-dom Agent Meta Process Mining — autonomous agent review and optimization recommendations #83)
• All 34 high severity alerts resolved (34 items listed above)
• @modelcontextprotocol/sdk updated to a version with session isolation fix
• hono updated to a version without JWT algorithm confusion
• axios updated past prototype pollution CVEs
• vite pinned to a patched version (dev server file-read fix)
• npm audit in src/frontend/ and src/mcp-server/ reports zero critical/high findings
• CI passes on updated lock files

Technical Notes

• Most alerts are duplicated (two entries = two affected manifests or lock files). A single package upgrade typically closes both.
• happy-dom is a test dependency — evaluate if it can be replaced with jsdom to eliminate the critical RCE surface entirely.
• hono and @hono/node-server are production runtime deps in src/mcp-server/ — prioritize these.
• rollup is a build-time dep; still warrants patching to prevent supply-chain CI attacks.
• After upgrading, run the full test suite: npm test in each sub-package and the Trinity API test suite.

Child Issues

Individual PRs/issues per package family may be opened as children of this umbrella. Reference this issue number in each PR body.

References

• Dependabot alerts: https://github.com/abilityai/trinity/security/dependabot

[vybe]

/claim

[github-actions]

Claimed by @vybe. Label status-in-progress added.

Next steps:

1. Create branch: feature/793-<short-slug>
2. Implement the feature
3. Open a PR with Fixes #793

[vybe]

Shipped in v0.6.0 (released via #998).