Configuring Continue.dev
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This guide details how to configure the Continue.dev extension running on a code-server instance to autonomously execute shell commands using the Model Context Protocol (MCP).

The Challenge
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By default, Continue’s chat interface is designed as a “human-in-the-loop” assistant. When asked to run a command, the LLM will typically generate a Markdown code block (e.g., ```bash). The Continue UI intercepts this and displays a “Run in Terminal” button, requiring the user to click it, which then pastes the command into the VS Code terminal.

Furthermore, in remote environments like code-server or VS Code Remote-SSH, Continue often struggles to reliably capture standard output (stdout) natively due to how remote terminals are spawned and monitored.

To achieve true autonomous agent behavior—where the LLM runs the command, reads the output, and continues working without user intervention—we must leverage an MCP server and forcefully override the LLM’s default prompting behavior.

The Solution: MCP + System Message Override
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To fix this, we need two main components:

An MCP Server: Specifically, shell-mcp-server (or similar), which exposes an execute_shell_command tool to the LLM.
An Aggressive System Message: We must inject a systemMessage into the Continue configuration that strictly forbids the generation of Markdown code blocks and mandates the use of the tool.

Step 1: Install the MCP Server
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Install a shell MCP server globally on the host machine running code-server.

npm install -g shell-mcp-server

Note: Depending on the specific package installed, you may need to ensure the script’s schema descriptions are in English and optimized for Linux (defaulting to /bin/bash instead of Windows cmd.exe) to prevent the LLM from getting confused.

Step 2: Configure Continue
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Update your Continue configuration file, typically located at ~/.continue/config.yaml or ~/.continue/config.json.

Here is a complete, detailed example configuration demonstrating the necessary setup:

# The display name of this workspace/configuration
name: Home Lab Config

# Config schema version
version: 1.0.0
schema: v1

# Define the Language Models available to Continue
models:
  # This is the primary model used for heavy lifting (chat, applying code edits)
  - name: Gemma-4-26B-Heavy
    provider: ollama
    model: gemma4:26b
    apiBase: http://10.0.0.109:11434
    roles:
      - chat
      - edit
      - apply
    # CRITICAL: MUST include 'tool_use' to allow the model to interact with MCP servers
    capabilities:
      - tool_use

  # A faster model for autocomplete functions
  - name: Gemma-4-E4B-Fast
    provider: ollama
    model: gemma4:e4b
    apiBase: http://10.0.0.109:11434
    roles:
      - chat
      - autocomplete
    capabilities:
      - tool_use

# Define the MCP Servers that provide tools to the LLM
mcpServers:
  - name: terminal
    # CRITICAL: Use absolute paths to the node binary and the MCP server script 
    # for maximum stability in code-server environments.
    command: /home/wompmacho/.nvm/versions/node/v24.14.0/bin/node
    args:
      - /home/wompmacho/.nvm/versions/node/v24.14.0/bin/shell-mcp-server

# Define context providers the LLM can use to gather information
context:
  - provider: file
  - provider: code
  - provider: terminal
  - provider: diff
  - provider: open
  - provider: currentFile

# Custom workspace rules to guide the LLM's general behavior
rules:
  - Always assume a Linux/Ubuntu environment for terminal commands
  - Use rules in /home/wompmacho/.gemini/GEMINI.md for all prompts
  - Use skills in /home/wompmacho/.gemini/skills
  - Evaluate if it makes sense to use any of the available skills for each prompt
  # A soft rule reinforcing the tool behavior
  - 'CRITICAL: When the user asks to run a command, NEVER generate a markdown code block for the user to run. You MUST autonomously use the MCP tool to execute the command directly to capture the output.'

# The System Message Override (The Secret Sauce)
# This strictly overrides Continue's core internal prompts which strongly bias towards Markdown code blocks.
systemMessage: 'You are an autonomous AI agent integrated into the developer''s workspace. You have access to MCP tools, including ''execute_shell_command''. ABSOLUTELY CRITICAL: Whenever the user asks you to run, execute, or check something via the terminal/shell, you MUST invoke the ''execute_shell_command'' tool immediately. DO NOT output the command in a markdown block (e.g. ```bash). DO NOT ask the user to run it themselves. You must call the tool, capture the output, and report the results back to the user.'

Key Takeaways
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Absolute Paths: In remote environments like code-server, always use absolute paths for the command and args in the mcpServers definition to avoid $PATH resolution errors when the extension spawns the subprocess.
capabilities: [tool_use]: Ensure your chosen model supports tool usage and that the capability is explicitly declared in your config.yaml.
The System Message: Continue’s internal prompt engineering is very persistent about keeping the human in the loop. The systemMessage must be highly aggressive and specifically ban Markdown block generation to successfully force the LLM to route its output through the MCP tool pipeline instead of the chat interface.

Configuring Continue.dev#

The Challenge#

The Solution: MCP + System Message Override#

Step 1: Install the MCP Server#

Step 2: Configure Continue#

Key Takeaways#