Atlas MCP Server

Thoth

Agentic systematic literature reviews with verifiable citations.

Named for Thoth, ancient Egypt's ibis-headed god of writing and scribes — the divine patron of the work this tool automates.

Live app: https://thoth-slr.vercel.app · Public evals: https://thoth-slr.vercel.app/evals · MCP endpoint: https://thoth-slr.vercel.app/api/mcp/mcp

Thoth turns a research question and a corpus of PDFs into an evidence-grounded literature review. A multi-step LangGraph agent (planner → retriever → assessor → drafter → critic) reads the papers, drafts the review, and runs a cite_check post-pass that verifies every cited claim against the source paper — flagging hallucinated citations before the user reads the draft.

Claude.ai connected to Thoth via the official MCP Registry. After list_reviews surfaces a review with faithfulness 0.13, Claude calls get_citation_audit and identifies all 6 unsupported claims — every one citing the same paper, with invented percentages that aren't in the source. Try it: Connect via MCP.

Verified engineering proofs

What makes Thoth different

1. cite_check post-pass. Every [paper_id] citation in the generated draft is verified against the cited paper before the user reads the draft. The MCP demo above shows Claude.ai using this audit to identify 6 hallucinated statistics in a real SLR draft on the ReAct paper.
2. Authenticated, registered MCP server. Most public MCP servers ship with no auth. Thoth uses OAuth 2.1 + PKCE + Dynamic Client Registration via Clerk (resource-server pattern, RFC 8707), with SHA-256 audit logs and DB-backed sliding-window rate limits. Listed in the official MCP Registry; works in claude.ai, Claude Desktop (via mcp-remote), Cursor, and MCP Inspector.
3. Public eval dashboard tied to main. Every commit can run the agent against a versioned golden set; results render at /evals. Designed so an eval regression is a public signal, not a hidden one.
4. 6 LLM providers, $0 default. Switch providers via one env var (LLM_PROVIDER=mistral|groq|gemini|anthropic|openai|claude-agent); Mistral free tier is the default. Local eval runs can use a Claude Max subscription via @anthropic-ai/claude-agent-sdk without an API key.

Connect via MCP

Thoth ships an authenticated MCP server at https://thoth-slr.vercel.app/api/mcp/mcp — paste this URL into claude.ai (Pro/Max), Claude Desktop, Cursor, or any MCP-compatible client. OAuth flow runs in your browser (powered by Clerk + Dynamic Client Registration); you never copy-paste a token.

Listed in the official MCP Registry as io.github.ahmedEid1/thoth. Verify independently with:

curl "https://registry.modelcontextprotocol.io/v0.1/servers?search=thoth" | jq '.servers[0].server'

Available tools (all read-only, all scoped to your Thoth account):

• list_reviews — list your Thoth reviews with critic + faithfulness scores
• get_review_draft — fetch the markdown draft of a completed review
• get_citation_audit — fetch the per-claim cite_check verdict report

See docs/mcp/tools.md for the full tool reference and docs/mcp/security.md for the auth + audit model.

Setting it up in claude.ai (Pro/Max — Connectors → Add custom connector → paste the URL → OAuth via Clerk + DCR, no manual client config needed):

Stack

Quickstart

git clone https://github.com/ahmedEid1/thoth.git
cd thoth
cp .env.example .env       # fill in Clerk + Trigger.dev keys + MISTRAL_API_KEY
docker compose up -d       # postgres :5433, minio :9010/:9011, langfuse :3030
pnpm install
pnpm prisma migrate dev
pnpm dev                   # Next.js on :3000
pnpm dev:trigger           # Trigger.dev worker (separate terminal)

See .env.example for the full env-var list. Non-obvious ones: S3_FORCE_PATH_STYLE=true for MinIO; CLERK_WEBHOOK_SIGNING_SECRET only when wiring Clerk's webhook in prod.

Tests

pnpm test                                                                # 199 unit/integration tests
PLAYWRIGHT_BASE_URL=https://thoth-slr.vercel.app pnpm playwright test tests/e2e/mcp-smoke.spec.ts  # 3 live e2e
pnpm tsx scripts/verify-mcp-audit.ts                                     # spot-check the McpCall audit log

LLM provider

Thoth uses Vercel AI SDK so you can swap providers via a single env var.

*Gemini Flash has a known parse issue with Vercel AI SDK structured output (vercel/ai#12187) — usable but unreliable for Thoth's per-call Zod schemas. Mistral is the default specifically because it's the most reliable free option for this workload.

Switch with LLM_PROVIDER=<name> in .env. Tier choice (smart/fast) per prompt stays the same — the dispatcher maps each tier to the equivalent model per provider (see lib/llm/tiers.ts).

Self-host alternative

Don't want to depend on Vercel + Neon + R2 + Langfuse Cloud? See docs/self-host/oracle-cloud-quickstart.md for a step-by-step walkthrough to deploy Thoth on Oracle Cloud's Always Free tier (4-core ARM Ampere A1 + 24 GB RAM, free forever). One VM runs Thoth + Postgres + MinIO + Langfuse behind Caddy with auto-TLS; you still use a hosted LLM API (Mistral free tier, or any of the 6 supported providers). Total recurring cost: $0/month + ~€10/yr domain. Config under infra/self-host/.

Built with spec-driven development

Every milestone is specified, planned, and reviewed before code. Specs live under docs/superpowers/specs/; per-milestone TDD plans under docs/superpowers/plans/. The release checklist is at RELEASING.md.

Roadmap & changelog

• M1 — Workspace foundation ✅ v0.1.0-m1 — Clerk auth, Prisma v7, S3 object store, PDF upload + Trigger.dev parse task
• M2 — Summarisation + Langfuse observability ✅ v0.2.0-m2 — lib/llm.ts wrapper, summarize-paper task, trace per call
• M3 — Full agent loop + HITL ✅ v0.3.0-m3 — LangGraph state machine + Trigger.dev durability + approve-plan / approve-papers gates
• M3.5a — LLM provider abstraction ✅ v0.3.5-m3.5a — Vercel AI SDK dispatcher, 4-provider adapters, tier mapping
• M3.5b — Cloud deploy ($0) ✅ v0.3.6-m3.5b — Vercel + Neon + R2 + Langfuse Cloud + Trigger.dev Cloud + Clerk Cloud
• M3.5c — Self-host fallback ✅ v0.6.0-m3.5c — Oracle Cloud Always Free walkthrough + infra/self-host/
• M4a — Critic + cite_check ✅ v0.4.0-m4a — LLM-as-judge critic loop + per-citation verification post-pass + ClaimCheck table
• M4b — Eval harness + public /evals ✅ v0.4.1-m4b — Headless graph runner, 4 metrics, public dashboard, regression gate
• v0.4.2 — Claude Agent SDK provider ✅ — Free programmatic Claude via Code CLI session (no API key), for local eval baselines
• v0.5.0 — Trigger.dev Cloud production deploy ✅ — All 3 background tasks on managed infra
• v0.5.1 — First live end-to-end review on prod ✅ — Real PDF (ReAct paper) → full SLR pipeline → completed draft + critic + cite_check
• v0.7.0-m5 — Authenticated MCP server ✅ — Streamable HTTP at /api/mcp/mcp, OAuth 2.1 + PKCE + DCR via Clerk, 3 read-only tools, audit log + rate limits, published to the official MCP Registry as io.github.ahmedEid1/thoth
• M6 (next) — 30-question real-paper golden eval set, recruiter 1-pager, public launch (HN / LinkedIn / Twitter)

License

MIT