Cortex MCP

Multi-level reasoning MCP server with configurable depth levels, session-based state management, structured thought input, and real-time trace resources.

Overview

Cortex MCP is a stdio-only MCP server for stateful, depth-controlled reasoning. The runtime entrypoint in src/index.ts connects createServer() to StdioServerTransport, and the server surface in src/server.ts enables tools, prompts, completions, logging, and subscribable resources around a single session-based reasoning engine.

The live MCP surface confirmed by Inspector is 1 tool, 6 concrete resources, 4 resource templates, and 7 prompts. Sessions are stored in memory, exposed as MCP resources, and cleared on process restart.

Key Features

• reasoning_think supports step-by-step sessions, run_to_completion batches, rollback, early conclusion, and structured observation / hypothesis / evaluation input.
• Four depth levels are built into the engine: basic, normal, high, and expert, each with bounded thought ranges and token budgets.
• Prompt helpers expose reasoning.basic, reasoning.normal, reasoning.high, reasoning.expert, reasoning.continue, reasoning.retry, and get-help.
• Resource endpoints expose internal docs plus live session lists, per-session JSON views, full markdown traces, and individual thought documents.
• Completions are wired for levels, session IDs, and thought names through completable() and resource-template completion hooks.

Requirements

• Node.js >=24 for local npx or npm usage.
• An MCP client that supports stdio transport.
• Optional: Docker if you want to build or run the container image defined by Dockerfile.

Quick Start

Use this standard MCP client configuration:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

Client Configuration

Add to .vscode/mcp.json:

{
  "servers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

Or install via CLI:

code --add-mcp '{"name":"cortex-mcp","command":"npx","args":["-y","@j0hanz/cortex-mcp@latest"]}'

For more info, see VS Code MCP docs.

Add to .vscode/mcp.json:

{
  "servers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

Or install via CLI:

code-insiders --add-mcp '{"name":"cortex-mcp","command":"npx","args":["-y","@j0hanz/cortex-mcp@latest"]}'

For more info, see VS Code Insiders MCP docs.

Add to ~/.cursor/mcp.json:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Cursor MCP docs.

Add to mcp.json (VS integrated):

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Visual Studio MCP docs.

Add to Goose extension registry:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Goose MCP docs.

Add to LM Studio MCP config:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see LM Studio MCP docs.

Add to claude_desktop_config.json:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Claude Desktop MCP docs.

Add to Claude Code CLI:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

Or install via CLI:

claude mcp add cortex-mcp -- npx -y @j0hanz/cortex-mcp@latest

For more info, see Claude Code MCP docs.

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Windsurf MCP docs.

Add to Amp MCP config:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

Or install via CLI:

amp mcp add cortex-mcp -- npx -y @j0hanz/cortex-mcp@latest

For more info, see Amp MCP docs.

Add to cline_mcp_settings.json:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Cline MCP docs.

Add to ~/.codex/config.yaml or codex CLI:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Codex CLI MCP docs.

Add to .vscode/mcp.json:

{
  "servers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see GitHub Copilot MCP docs.

Add to Warp MCP config:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Warp MCP docs.

Add to .kiro/settings/mcp.json:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Kiro MCP docs.

Add to ~/.gemini/settings.json:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Gemini CLI MCP docs.

Add to ~/.config/zed/settings.json:

{
  "context_servers": {
    "cortex-mcp": {
      "settings": {
        "command": "npx",
        "args": ["-y", "@j0hanz/cortex-mcp@latest"]
      }
    }
  }
}

For more info, see Zed MCP docs.

Add to VS Code settings.json:

Add to your VS Code settings.json under augment.advanced.

{
  "augment.advanced": {
    "mcpServers": [
      {
        "id": "cortex-mcp",
        "command": "npx",
        "args": ["-y", "@j0hanz/cortex-mcp@latest"]
      }
    ]
  }
}

For more info, see Augment MCP docs.

Add to Roo Code MCP settings:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Roo Code MCP docs.

Add to Kilo Code MCP settings:

{
  "mcpServers": {
    "cortex-mcp": {
      "command": "npx",
      "args": ["-y", "@j0hanz/cortex-mcp@latest"]
    }
  }
}

For more info, see Kilo Code MCP docs.

Use Cases

Start bounded reasoning at the right depth

Use reasoning.basic, reasoning.normal, reasoning.high, or reasoning.expert when the client wants a prompt-first entrypoint, or call reasoning_think directly with query, level, and the first thought. Each response returns the current session state plus a summary string that tells the client how to continue.

Relevant tool: reasoning_think
Related prompts: reasoning.basic, reasoning.normal, reasoning.high, reasoning.expert

Continue, retry, or batch an active session

Reuse sessionId to continue a prior trace, switch to runMode="run_to_completion" when you already have the remaining thought inputs, or use the continuation and retry prompts to generate the next call payload. The handler also supports rollbackToStep and isConclusion for revising or ending a trace early.

Relevant tool: reasoning_think
Related prompts: reasoning.continue, reasoning.retry

Inspect live traces without re-running the tool

Read reasoning://sessions for the active session list, reasoning://sessions/{sessionId} for the JSON detail view, reasoning://sessions/{sessionId}/trace for the markdown transcript, or reasoning://sessions/{sessionId}/thoughts/{thoughtName} for a single thought. This lets a client present progress or audit a session independently from the next tool call.

Relevant resources: reasoning://sessions, reasoning://sessions/{sessionId}, reasoning://sessions/{sessionId}/trace, reasoning://sessions/{sessionId}/thoughts/{thoughtName}

Architecture

[MCP Client]
    |
    | stdio
    v
[src/index.ts]
    createServer()
    -> new StdioServerTransport()
    -> server.connect(transport)
    |
    v
[src/server.ts]
    McpServer("cortex-mcp")
    capabilities:
      - tools
      - prompts
      - completions
      - logging
      - resources { subscribe: true, listChanged: true }
    |
    +--> tools/call
    |     -> reasoning_think
    |     -> src/tools/reasoning-think.ts
    |     -> ReasoningThinkInputSchema / ReasoningThinkToolOutputSchema
    |     -> src/engine/reasoner.ts
    |     -> SessionStore
    |
    +--> prompts/get
    |     -> src/prompts/index.ts
    |
    +--> resources/read
    |     -> src/resources/index.ts
    |     -> internal://* and reasoning://sessions/*
    |
    +--> notifications
          -> logging messages
          -> resources/list_changed
          -> resources/updated
          -> notifications/progress

Request Lifecycle

[Client] -- initialize --> [Server]
[Server] -- serverInfo + capabilities --> [Client]
[Client] -- notifications/initialized --> [Server]
[Client] -- tools/call {name: "reasoning_think", arguments} --> [Handler]
[Handler] -- validate args --> [Reasoner + SessionStore]
[Reasoner] -- progress/resource events --> [Server notifications]
[Handler] -- structuredContent + optional trace resource --> [Client]

MCP Surface

Tools

reasoning_think

Stateful reasoning tool for creating and continuing multi-step sessions. It supports one-step interactive calls, run_to_completion batches, structured observation/hypothesis/evaluation input, rollback, and early conclusion while returning structured session state.

| Parameter | Type | Required | Description | | ---------------- | --------- | -------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | query | string | no | Question or problem to analyze. | | level | string | no | Depth level. Required for new sessions. basic (1–3 steps, 2K budget), normal (4–8 steps, 8K budget), high (10–15 steps, 32K budget), expert (20–25 steps, 128K budget). | | targetThoughts | integer | no | Exact step count. Must fit level range. | | sessionId | string | no | Session ID to continue. | | runMode | string | no | "step" (default) or "run_to_completion". | | thought | any | no | Reasoning text. Stored verbatim. String for step mode, string[] for batch. | | isConclusion | boolean | no | End session early at final answer. | | rollbackToStep | integer | no | 0-based index to rollback to. Discards later thoughts. | | stepSummary | string | no | One-sentence step summary. | | observation | string | no | Known facts at this step. | | hypothesis | string | no | Proposed next idea. | | evaluation | string | no | Critique of hypothesis. |

1. [Client] -- tools/call {name: "reasoning_think", arguments} --> [Server]
   Transport: stdio
2. [Server] -- dispatch("reasoning_think") --> [Handler: src/tools/reasoning-think.ts]
3. [Handler] -- validate(ReasoningThinkInputSchema) --> [src/engine/reasoner.ts]
4. [Reasoner] -- create/update session --> [src/engine/session-store.ts]
5. [Handler] -- structuredContent + optional embedded trace resource --> [Client]

Resources

| Resource | URI or Template | MIME Type | Description | | --------------------------- | --------------------------------------------------------- | ------------------ | -------------------------------------------------------------------------------------------- | | server-instructions | internal://instructions | text/markdown | Usage instructions for the MCP server. | | server-config | internal://server-config | application/json | Runtime limits and level configurations for the reasoning server. | | tool-catalog | internal://tool-catalog | text/markdown | Tool reference: models, params, outputs, data flow. | | tool-info | internal://tool-info/{toolName} | text/markdown | Per-tool contract details. | | tool-info-reasoning_think | internal://tool-info/reasoning_think | text/markdown | Contract details for reasoning_think. | | workflows | internal://workflows | text/markdown | Recommended workflows and tool sequences. | | reasoning.sessions | reasoning://sessions | application/json | List of active reasoning sessions with summaries. Updated in real-time as sessions progress. | | reasoning.session | reasoning://sessions/{sessionId} | application/json | Detailed view of a single reasoning session, including all thoughts and metadata. | | reasoning.trace | reasoning://sessions/{sessionId}/trace | text/markdown | Markdown trace of a reasoning session (full content). | | reasoning.thought | reasoning://sessions/{sessionId}/thoughts/{thoughtName} | text/markdown | Markdown content of a single thought (for example Thought-1). |

Prompts

| Prompt | Arguments | Description | | -------------------- | ------------------------------------------------------------- | ------------------------------------------------------- | | get-help | none | Return server usage instructions. | | reasoning.basic | query required, targetThoughts optional | Basic-depth reasoning (1-3 thoughts). | | reasoning.normal | query required, targetThoughts optional | Normal-depth reasoning (4-8 thoughts). | | reasoning.high | query required, targetThoughts optional | High-depth reasoning (10-15 thoughts). | | reasoning.expert | query required, targetThoughts optional | Expert-depth reasoning (20-25 thoughts). | | reasoning.continue | sessionId required, query optional, level optional | Continue an existing session. Optional follow-up query. | | reasoning.retry | query required, level required, targetThoughts optional | Retry a failed reasoning task with modified parameters. |

MCP Capabilities

| Capability | Status | Evidence | | ------------------------ | --------- | ----------------------------------------------------------------------------- | | tools | confirmed | src/server.ts:203-205, src/tools/reasoning-think.ts:479 | | prompts | confirmed | src/server.ts:205, src/prompts/index.ts:201 | | completions | confirmed | src/server.ts:207, src/prompts/index.ts:249, src/resources/index.ts:375 | | logging | confirmed | src/server.ts:204, src/server.ts:98 | | resources.subscribe | confirmed | src/server.ts:208, src/server.ts:121 | | resources.listChanged | confirmed | src/server.ts:208, src/server.ts:114 | | progress notifications | confirmed | src/lib/mcp.ts:71, src/tools/reasoning-think.ts:424 |

Tool Annotations

| Annotation | Value | Evidence | | ----------------- | ------- | ---------------------------------- | | readOnlyHint | false | src/tools/reasoning-think.ts:500 | | destructiveHint | false | src/tools/reasoning-think.ts:502 | | openWorldHint | false | src/tools/reasoning-think.ts:503 | | idempotentHint | false | src/tools/reasoning-think.ts:501 |

Structured Output

• reasoning_think declares outputSchema and returns structuredContent, with an embedded trace resource when the trace is small enough. Evidence: src/tools/reasoning-think.ts:498, src/lib/mcp.ts:97-114.

Configuration

| Variable | Default | Required | Evidence | | ----------------------------------- | ---------------------- | -------- | ------------------------------------------------------------- | | CORTEX_SESSION_TTL_MS | 1800000 (30 minutes) | no | src/engine/reasoner.ts:22, src/engine/session-store.ts:19 | | CORTEX_MAX_SESSIONS | 100 | no | src/engine/reasoner.ts:23, src/engine/session-store.ts:20 | | CORTEX_MAX_TOTAL_TOKENS | 2000000 | no | src/engine/reasoner.ts:24, src/engine/session-store.ts:21 | | CORTEX_MAX_ACTIVE_REASONING_TASKS | 32 | no | src/engine/config.ts:41-44 | | CORTEX_REDACT_TRACE_CONTENT | false | no | src/engine/config.ts:21 |

[!NOTE] The source does not define any HTTP host/port configuration. The only other environment-related signal is NODE_ENV=production in the Docker image and --env-file=.env in the local dev:run script.

Security

| Control | Status | Evidence | | ---------------------------- | --------- | ----------------------------------------------------------------------------------- | | input validation | confirmed | src/schemas/inputs.ts:13, src/schemas/outputs.ts:46, src/prompts/index.ts:207 | | stdout-safe logging fallback | confirmed | src/server.ts:98, src/server.ts:145 | | main-thread-only runtime | confirmed | src/index.ts:15-25 | | non-root container user | confirmed | Dockerfile:37 |

[!NOTE] No auth, OAuth, HTTP origin checks, or rate-limiting controls are implemented in the current source because the server only exposes stdio transport.

Development

| Script | Command | Purpose | | ---------------- | --------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------- | | dev | tsc --watch --preserveWatchOutput | Watch and compile source during development. | | dev:run | node --env-file=.env --watch dist/index.js | Run the built server in watch mode with an optional local .env file. | | build | node scripts/tasks.mjs build | Clean dist, compile TypeScript, copy assets, and make the entrypoint executable. | | lint | eslint . | Run ESLint across the repository. | | type-check | node scripts/tasks.mjs type-check | Run source and test TypeScript checks concurrently. | | test | node scripts/tasks.mjs test | Run the TypeScript test suites with the configured loader. | | test:dist | node scripts/tasks.mjs test:dist | Rebuild first, then run tests against the built output. | | test:fast | node --test --import tsx/esm src/__tests__/**/*.test.ts node-tests/**/*.test.ts | Run the fast direct test command without the task wrapper. | | format | prettier --write . | Format the repository. | | inspector | npm run build && npx -y @modelcontextprotocol/inspector node dist/index.js | Build the server and open it in the MCP Inspector. | | prepublishOnly | npm run lint && npm run type-check && npm run build | Enforce release checks before publishing. |

Additional helper scripts for diagnostics, coverage, asset copying, and knip are defined in package.json.

Build and Release

• .github/workflows/release.yml bumps package.json and server.json, then runs npm run lint, npm run type-check, npm run test, and npm run build before tagging and creating a GitHub release.
• The same workflow publishes the package to npm with Trusted Publishing, publishes to the MCP Registry with mcp-publisher, and pushes a multi-arch Docker image to ghcr.io.
• Dockerfile uses a multi-stage Node 24 Alpine build, prunes dev dependencies, and runs the released container as the mcp user.

Troubleshooting

• Sessions are in memory and expire after 30 minutes by default. If you receive E_SESSION_NOT_FOUND, start a new session or increase CORTEX_SESSION_TTL_MS.
• runMode="run_to_completion" requires enough thought entries to cover the remaining steps. If you want the server to return after each step, keep the default step mode.
• For stdio transport, do not add custom stdout logging around the server process. This server routes logs through MCP logging and falls back to stderr on failures.

Credits

| Dependency | Registry | | ------------------------------------------------------------------------------------ | -------- | | @modelcontextprotocol/sdk | npm | | zod | npm |

Contributing and License

• License: MIT
• Contributions are welcome via pull requests.