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Research-Stack/.mcp.json
allaun 475f6319ea chore(repo): push local 768-commit branch state onto clean remote baseline 
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{
"$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 that appear in distilled docs and ArithmeticSpec. Backed by sympy-mcp upstream; see https://github.com/sdiehl/sympy-mcp.",
"command": "uv",
"args": [
"tool",
"run",
"--from",
"sympy-mcp",
"sympy-mcp"
],
"env": {}
},
"wolfram-alpha": {
"_comment": "Wolfram Alpha symbolic verification. Provide WOLFRAM_ALPHA_APPID in the shell environment before starting Devin/opencode. The server starts regardless and will error on individual tool calls if the key is absent — MCP startup is not blocked.",
"command": "npx",
"args": [
"-y",
"@wolfram-alpha/mcp-server"
],
"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"
},
"aws": {
"_comment": "AWS API MCP server (awslabs.aws-api-mcp-server). Provides broad AWS CLI/API access via boto3 credential chain (default profile, us-east-1). Credentials are read from ~/.aws — no secrets embedded here.",
"command": "uvx",
"args": [
"awslabs.aws-api-mcp-server@latest"
],
"env": {
"AWS_REGION": "us-east-1",
"FASTMCP_LOG_LEVEL": "ERROR"
}
},
"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).",
"command": "uvx",
"args": [
"lean-mcp",
"--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": "http://54.236.176.28:8787",
"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 — 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": {
"command": "npx",
"args": [
"--prefer-online",
"-y",
"@contextstream/mcp-server@latest"
],
"env": {
"CONTEXTSTREAM_API_URL": "https://api.contextstream.io",
"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": "false",
"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 — 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"
}
}
}
}
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