{
  "$schema": "https://modelcontextprotocol.io/schemas/2025-03-26/client-config.json",
  "_comment": "Math-first MCP server declarations for Research Stack. Each server below is gated on a runtime environment variable so the config never embeds secrets and so contributors who have not provisioned a given backend simply skip it. See docs/math-first-tooling.md for setup instructions.",
  "mcpServers": {
    "filesystem": {
      "_comment": "Read/write proof artifacts, Lean kernels, and DeepSeek receipts. Scope is the repository root so review tooling cannot escape the project tree.",
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "."
      ],
      "env": {}
    },
    "sympy": {
      "_comment": "Local SymPy bridge for symbolic verification of arithmetic claims. Package is 'mcp-sympy' on PyPI (provides 'mcp-sympy' executable); the sdiehl/sympy-mcp GitHub name differs from the PyPI name.",
      "command": "uvx",
      "args": [
        "mcp-sympy"
      ],
      "env": {}
    },
    "wolfram-alpha": {
      "_comment": "Wolfram Alpha symbolic verification. Requires WOLFRAM_APP_ID in the shell environment (NOT WOLFRAM_ALPHA_APPID \u2014 that's an alias in fish config). Package is 'wolfram-mcp' on npm (was '@wolfram-alpha/mcp-server' which no longer exists).",
      "command": "npx",
      "args": [
        "-y",
        "wolfram-mcp"
      ],
      "env": {}
    },
    "notion": {
      "_comment": "Notion integration via official Notion MCP (Streamable HTTP + OAuth). Run `devin mcp login notion` once to complete the OAuth flow; tokens are stored locally and auto-refreshed.",
      "url": "https://mcp.notion.com/mcp",
      "transport": "http"
    },
    "lean": {
      "_comment": "Lean 4 / Mathlib typecheck bridge. Targets 0-Core-Formalism/lean/Semantics/ via the existing lakefile. Requires `elan` on PATH; see GETTING_STARTED.md for the lean-toolchain pin (leanprover/lean4:v4.30.0-rc2). The executable in the lean-mcp package is 'lean-mcp-server', not 'lean-mcp'.",
      "command": "uvx",
      "args": [
        "--from",
        "lean-mcp",
        "lean-mcp-server",
        "--lakefile",
        "0-Core-Formalism/lean/Semantics/lakefile.toml"
      ],
      "env": {}
    },
    "remote-lean-proof": {
      "_comment": "Hermes/OpenCode/Codex proof backend. Calls the dedicated AWS language-proof-server and returns receipt-bearing Lean/Lake results. Token is read from PROOF_SERVER_TOKEN or ~/.config/ene/language-proof-server.token.",
      "command": "python3",
      "args": [
        "4-Infrastructure/infra/remote_lean_proof_mcp.py"
      ],
      "env": {
        "PROOF_SERVER_URL": "${PROOF_SERVER_URL}",
        "PROOF_SERVER_TOKEN_FILE": "/home/allaun/.config/ene/language-proof-server.token"
      }
    },
    "service-orchestrator": {
      "_comment": "Unified control plane: register/unregister services across Authentik + Caddy + credential server. Requires AUTHENTIK_TOKEN and CADDY_ADMIN env vars. HTTP mode on port 8338.",
      "command": "python3",
      "args": [
        "4-Infrastructure/infra/service-orchestrator/service_orchestrator.py"
      ],
      "env": {
        "AUTHENTIK_BASE": "http://100.102.173.61:9000",
        "CADDY_ADMIN": "http://100.101.247.127:2019",
        "CREDENTIAL_SERVER": "http://100.101.247.127:8444"
      }
    },
    "authentik-mcp": {
      "_comment": "Authentik SSO MCP server \u2014 user/group/application management via Authentik API v3. Requires AUTHENTIK_TOKEN env var. Built from 4-Infrastructure/shim/authentik_agent_manager/.",
      "command": "/home/allaun/Research Stack/4-Infrastructure/shim/authentik_agent_manager/target/release/mcp_server",
      "args": [],
      "env": {}
    },
    "contextstream": {
      "_comment": "Persistent memory, context, and search across all coding sessions. Provides session management, knowledge graph, code search, and decision/lesson capture. Plan: Elite.",
      "command": "npx",
      "args": [
        "--prefer-online",
        "-y",
        "@contextstream/mcp-server@latest"
      ],
      "env": {
        "CONTEXTSTREAM_API_URL": "https://api.contextstream.io",
        "CONTEXTSTREAM_API_KEY": "${CONTEXTSTREAM_API_KEY}",
        "CONTEXTSTREAM_ALLOW_HEADER_AUTH": "false",
        "CONTEXTSTREAM_WORKSPACE_ID": "21c133f6-6854-4e81-b801-4037c11b7e34",
        "CONTEXTSTREAM_PROJECT_ID": "ef91cc79-aae3-4765-ae0d-63b48f5ea6e6",
        "CONTEXTSTREAM_USER_AGENT": "contextstream-mcp/0.4.74",
        "CONTEXTSTREAM_TOOLSET": "complete",
        "CONTEXTSTREAM_LOG_LEVEL": "quiet",
        "CONTEXTSTREAM_OUTPUT_FORMAT": "compact",
        "CONTEXTSTREAM_CONTEXT_PACK": "true",
        "CONTEXTSTREAM_TRANSCRIPTS_ENABLED": "true",
        "CONTEXTSTREAM_HOOK_TRANSCRIPTS_ENABLED": "true",
        "CONTEXTSTREAM_SHOW_TIMING": "false",
        "CONTEXTSTREAM_PROGRESSIVE_MODE": "false",
        "CONTEXTSTREAM_ROUTER_MODE": "false",
        "CONTEXTSTREAM_CONSOLIDATED": "true",
        "CONTEXTSTREAM_AUTO_HIDE_INTEGRATIONS": "true",
        "CONTEXTSTREAM_SEARCH_LIMIT": "15",
        "CONTEXTSTREAM_SEARCH_MAX_CHARS": "2400",
        "CONTEXTSTREAM_INCLUDE_STRUCTURED_CONTENT": "true"
      }
    },
    "ene-contextstream": {
      "_comment": "Local ENE replacement for ContextStream-like memory/search/session recall. Writes local receipt-bearing SQLite memory and reads ene-api/session-sync when running.",
      "command": "python3",
      "args": [
        "/home/allaun/Research Stack/4-Infrastructure/infra/ene_contextstream_mcp.py"
      ],
      "env": {
        "ENE_API_URL": "http://127.0.0.1:3000",
        "ENE_CONTEXT_STORE": "/home/allaun/.local/share/ene/contextstream.sqlite",
        "ENE_CONTEXT_CANDIDATE_ROOT": "/home/allaun/Research Stack/shared-data/data/germane/research/github-ene-contextstream"
      }
    },
    "deepseek-prover": {
      "_comment": "DeepSeek-Prover-V2-7B proof search. Backend: ollama (default), huggingface, or deepseek_api. Generates Lean proof candidates, compiles with lake build, iterates with error feedback.",
      "command": "python3",
      "args": [
        "4-Infrastructure/infra/deepseek_prover_mcp.py"
      ],
      "env": {
        "DEEPSEEK_PROVER_BACKEND": "ollama",
        "OLLAMA_URL": "http://localhost:11434",
        "LAKE_WORKDIR": "/home/allaun/Research Stack/0-Core-Formalism/lean/Semantics"
      }
    },
    "vikunja": {
      "_comment": "Kanban board server on neon (100.92.88.64). Agents and humans set goals, track status, assign tasks. Wraps Vikunja v2.3.0 REST API.",
      "command": "python3",
      "args": [
        "4-Infrastructure/infra/vikunja_mcp.py"
      ],
      "env": {
        "VIKUNJA_URL": "http://100.92.88.64:3456",
        "VIKUNJA_TOKEN_FILE": "/home/allaun/.config/ene/vikunja.token"
      }
    },
    "lean-lsp": {
      "_comment": "Lean Language Server MCP \u2014 lightweight type-checking and proof info for Lean files in Semantics/.",
      "command": "uvx",
      "args": [
        "lean-lsp-mcp",
        "--lean-project-path",
        "0-Core-Formalism/lean/Semantics"
      ],
      "env": {}
    },
    "k8s": {
      "_comment": "Kubernetes MCP server (read-only). Query k3s cluster on cupfox (100.72.130.76). Uses default kubeconfig.",
      "command": "npx",
      "args": [
        "-y",
        "kubernetes-mcp-server@latest",
        "--read-only"
      ],
      "env": {}
    },
    "arxiv": {
      "_comment": "ArXiv paper search MCP. Cache papers in ~/.arxiv-papers for offline reference. Connects to the arxiv cross-ref pipeline.",
      "command": "uvx",
      "args": [
        "arxiv-mcp-server",
        "--storage-path",
        "/home/allaun/.arxiv-papers"
      ],
      "env": {}
    },
    "nixos": {
      "_comment": "NixOS MCP server. Read/write NixOS configs (steamdeck, nixos-laptop, neon). Requires ssh access.",
      "command": "uvx",
      "args": [
        "mcp-nixos"
      ],
      "env": {}
    },
    "shape-index": {
      "_comment": "FAMM shape-index of the Lean corpus. 112K indexed theorems classified by Sidon sumset signature. Query nearest neighbors by shape to find proof templates.",
      "command": "python3",
      "args": [
        "4-Infrastructure/infra/shape_index_mcp.py"
      ],
      "env": {
        "SHAPE_INDEX_PATH": "/home/allaun/lean_corpus/shape_index.json"
      }
    },
    "github": {
      "_comment": "GitHub MCP (official Copilot endpoint). Provides PR creation/review, issue tracking, CI status, repo search, and branch management. Set GITHUB_PERSONAL_ACCESS_TOKEN in the shell environment (token lives in Goose config \u2014 do NOT hardcode here). The token in ~/.config/goose/config.yaml should be migrated to a secrets store or shell profile.",
      "type": "http",
      "url": "https://api.githubcopilot.com/mcp/",
      "headers": {
        "Authorization": "Bearer ${GITHUB_PERSONAL_ACCESS_TOKEN}"
      }
    },
    "git": {
      "_comment": "Git MCP server for history navigation: diff, blame, log traversal, commit search. Complements the filesystem MCP with git-native operations. Useful for proof archaeology and tracing when/why a lemma changed.",
      "command": "uvx",
      "args": [
        "mcp-server-git",
        "--repository",
        "."
      ],
      "env": {}
    },
    "fetch": {
      "_comment": "HTTP fetch MCP \u2014 retrieve any public URL as text or markdown. Fills the gap between ArXiv (papers) and Wolfram (symbolic): reading Mathlib4 docs, Lean release notes, RFC pages, blog posts, etc.",
      "command": "uvx",
      "args": [
        "mcp-server-fetch"
      ],
      "env": {}
    },
    "serena": {
      "_comment": "Serena code intelligence MCP (Oraios). LSP-powered cross-file symbol search, call-graph navigation, and definition lookup across all languages in the Research Stack (Lean, Rust, Python). Complements lean-lsp (Lean-only) with multi-language awareness.",
      "command": "uvx",
      "args": [
        "--from",
        "git+https://github.com/oraios/serena",
        "serena",
        "start-mcp-server"
      ],
      "env": {}
    },
    "context7": {
      "_comment": "Context7 live library documentation (Upstash). Fetches real-time docs for Mathlib4, Lean stdlib, Python packages, and Rust crates \u2014 not stale training data. Use when lean-lsp hover info isn't enough and you need full API context.",
      "command": "npx",
      "args": [
        "-y",
        "@upstash/context7-mcp"
      ],
      "env": {}
    },
    "chrome-devtools": {
      "_comment": "Chrome DevTools MCP \u2014 control and inspect a live Chrome browser session. Useful for testing web UIs (Authentik admin, Vikunja, Grafana dashboards) and scraping dynamically rendered pages that fetch MCP cannot reach.",
      "command": "npx",
      "args": [
        "-y",
        "chrome-devtools-mcp@latest"
      ],
      "env": {}
    },
    "council-of-mine": {
      "_comment": "LLM council with 9 distinct personas (Block/Square). Routes a question to multiple opinionated advisors and synthesizes a debate. Useful for architectural decisions, proof strategy reviews, and doctrine alignment checks where a single agent perspective is insufficient.",
      "command": "uvx",
      "args": [
        "--from",
        "git+https://github.com/block/mcp-council-of-mine",
        "mcp_council_of_mine"
      ],
      "env": {}
    },
    "gdrive": {
      "_comment": "Google Drive MCP \u2014 read/write access to Google Drive files. Imported from Windsurf config. Requires GOOGLE_CLIENT_ID and GOOGLE_CLIENT_SECRET env vars.",
      "command": "npx",
      "args": [
        "-y",
        "@piotr-agier/google-drive-mcp"
      ],
      "env": {
        "GOOGLE_CLIENT_ID": "${GOOGLE_CLIENT_ID}",
        "GOOGLE_CLIENT_SECRET": "${GOOGLE_CLIENT_SECRET}"
      }
    },
    "pist-trace-classify": {
      "_comment": "PIST trace classifier MCP \u2014 from OpenCode config. Classifies braid traces using PIST geometry.",
      "command": "python3",
      "args": [
        "4-Infrastructure/shim/pist_trace_classify_mcp.py"
      ],
      "env": {
        "RDS_HOST": "${RDS_HOST}",
        "RDS_PORT": "${RDS_PORT}",
        "RDS_USER": "${RDS_USER}",
        "RDS_DB": "${RDS_DB}",
        "RDS_IAM_AUTH": "${RDS_IAM_AUTH}",
        "AWS_REGION": "${AWS_REGION}"
      }
    },
    "opencode-prover": {
      "_comment": "OpenCode Prover MCP \u2014 from OpenCode config. Lean proof verification bridge for OpenCode/Codex CLI.",
      "command": "python3",
      "args": [
        "5-Applications/tools-scripts/mcp/opencode_prover_mcp.py"
      ],
      "env": {}
    },
    "token-saver": {
      "_comment": "Token saver MCP \u2014 from OpenCode config. Saves tokens by consolidating file reads and reducing redundant context.",
      "command": "python3",
      "args": [
        "5-Applications/tools-scripts/mcp/token_saver_mcp.py"
      ],
      "env": {}
    },
    "container-use": {
      "_comment": "Container Use MCP (container-use.com). Spawns isolated container environments for running untrusted code, reproducible build experiments, and testing NixOS derivations without touching the host. Connects via mcp-remote relay.",
      "command": "npx",
      "args": [
        "-y",
        "mcp-remote",
        "https://container-use.com/mcp"
      ],
      "env": {}
    },
    "consensus": {
      "_comment": "Consensus MCP server for evidence-based search over 200M academic papers.",
      "url": "https://mcp.consensus.app/mcp",
      "transport": "http"
    }
  }
}