Keeping MCP Server config in sync between VS Code and GitHub Copilot CLI

Hey awesome people,

Over the last weeks, I’ve been jumping between VS Code and Copilot CLI a lot more than usual. One thing kept annoying me: my MCP setup was perfect in VS Code, but I had to keep tweaking pieces again in CLI.

If that sounds familiar, good news: if you already have MCP servers working in VS Code, you can reuse most of that setup in GitHub Copilot CLI.

In this post, I’ll show you the fastest way to ‘keep both in sync’ from VS Code mcp.json to Copilot CLI mcp-config.json, with the necessary commands for both PowerShell and Bash.

Why this matters

When you move between VS Code and terminal workflows, you really don’t want to rebuild MCP config from scratch every time.

I made that mistake once (probably multiple times, but didn’t want to exagerate too much…), and it was exactly as fun as it sounds: tiny syntax differences, one invalid server name, one missing env var, and suddenly you’re troubleshooting config instead of actually building. (Although I can tell you that this would be a perfect use case for GenAI GitHub Copilot, lol)

This guide helps you:

• keep one consistent MCP setup style (VSCode MCP Config as the ‘main’ source)
• avoid common config parsing errors in Copilot CLI
• ‘keep-in-sync’ in a few minutes, even if you’re new to MCP

MCP in plain English

MCP (Model Context Protocol) lets AI tools connect to external capabilities.

Think of MCP servers as “skill plugins” for your assistant, like:

• documentation search
• GitHub actions (issues, PRs, code search)
• browser automation
• Azure DevOps operations

File locations you should know

VS Code MCP config is typically found at:

• Workspace: ./mcp.json or ./.vscode/mcp.json
• User-level:
  • Windows: %APPDATA%\\Code\\User\\mcp.json
  • macOS: ~/Library/Application Support/Code/User/mcp.json
  • Linux: ~/.config/Code/User/mcp.json

Copilot CLI MCP config lives here on all platforms:

• ~/.copilot/mcp-config.json

VS Code vs Copilot CLI: the important differences

The two formats are very close, but not identical:

1. Top-level key

   • VS Code: servers
   • Copilot CLI: mcpServers

2. Server ID naming rules in Copilot CLI

   • allowed: letters, numbers, _, -
   • server keys with / must be renamed

3. VS Code inputs

   • supported in VS Code flow
   • not used in Copilot CLI config

4. Placeholder syntax

   • VS Code often uses ${env:VAR} and ${input:name}
   • Copilot CLI expects $VAR and supports explicit env mappings

None of this is hard, but it’s just different enough to break things when done manually in a hurry.

Fast path (recommended): automate conversion

You can grab both scripts directly from my GitHub repo:

• https://github.com/petender/MCP-Clone_VSCode2CLI

Quick clone commands (PowerShell, bash, zsh):

git clone https://github.com/petender/MCP-Clone_VSCode2CLI.git
cd MCP-Clone_VSCode2CLI

Use one of these scripts:

• convert-mcp-config.ps1 (Windows/macOS/Linux with pwsh)
• convert-mcp-config.sh (macOS/Linux with bash + python3)

I personally use the PowerShell version most of the time, no surprise I’m primarily a Windows-guy, but didn’t want to assume everyone is using PowerShell nowadays. (You should though ;)

What the script converts automatically

• servers -> mcpServers
• removes VS Code-only inputs
• converts ${input:name} -> $NAME
• converts ${env:VAR} -> $VAR
• adds/merges env mappings like "VAR": "$VAR"
• renames invalid server IDs (for example containing /)

This is exactly the part that saves the most time (and avoids the most headaches).

PowerShell usage (convert-mcp-config.ps1)

The script supports cross-platform defaults using your home path.

Easiest mode

pwsh -ExecutionPolicy Bypass -File ./convert-mcp-config.ps1

This auto-discovers common input locations and writes to ~/.copilot/mcp-config.json.

Explicit input, default output

pwsh -ExecutionPolicy Bypass -File ./convert-mcp-config.ps1 \
  -InputPath ./mcp.json

Explicit input and output

pwsh -ExecutionPolicy Bypass -File ./convert-mcp-config.ps1 \
  -InputPath ./mcp.json \
  -OutputPath ~/.copilot/mcp-config.json

Custom home path

pwsh -ExecutionPolicy Bypass -File ./convert-mcp-config.ps1 \
  -InputPath ./mcp.json \
  -UserHome /home/<user>

Bash usage (convert-mcp-config.sh)

First run:

chmod +x ./convert-mcp-config.sh

Easiest mode

./convert-mcp-config.sh

Explicit input, default output

./convert-mcp-config.sh --input ./mcp.json

Explicit input and output

./convert-mcp-config.sh --input ./mcp.json --output ~/.copilot/mcp-config.json

Custom home path

./convert-mcp-config.sh --input ./mcp.json --user-home /home/<user>

Bash prerequisites

• bash
• python3

Verify in Copilot CLI

After conversion, open Copilot CLI and run:

1. /mcp reload
2. /mcp show

If your config is valid, your servers should load without parsing errors.

If they don’t show up right away, don’t panic. In most cases it’s either naming rules or env vars (both covered below).

Required environment variables (for the sample config)

Set these before launching Copilot CLI:

• GITHUB_PERSONAL_ACCESS_TOKEN
• ADO_ORG
• ADO_DOMAIN

PowerShell session example:

$env:GITHUB_PERSONAL_ACCESS_TOKEN = "<your_token>"
$env:ADO_ORG = "<your_ado_org>"
$env:ADO_DOMAIN = "core"

bash/zsh example:

export GITHUB_PERSONAL_ACCESS_TOKEN="<your_token>"
export ADO_ORG="<your_ado_org>"
export ADO_DOMAIN="core"

Manual conversion checklist

If you want to edit by hand, follow this sequence:

• rename servers to mcpServers
• remove inputs
• replace ${input:name} with $NAME
• replace ${env:VAR} with $VAR and add/update env
• rename server IDs that contain unsupported characters
• keep operational properties unchanged (type, command, args, url, version, gallery)

This checklist is also useful as a review checklist in PRs.

Common errors and quick fixes

MCP server name must only contain alphanumeric characters, underscores, and hyphens

Cause: a server key still contains / (or another invalid character).

Fix example:

• microsoft/playwright-mcp -> microsoft_playwright_mcp

Server starts but fails with auth/runtime errors

Cause: missing or wrong environment variable values.

Fix:

• validate variable names exactly
• confirm values exist in the active shell session
• run /mcp reload again

Also make sure you start Copilot CLI from the same shell/session where variables are set.

command not found

Cause: one of the required tools is missing.

Fix:

• install dependencies used by your config (docker, npx, uvx, etc.)

Summary

Most VS Code MCP config can be reused in Copilot CLI. The key differences are server ID naming, top-level key name, and placeholder handling.

While one could assume that the MCP Configuration should be standardized across platforms, once I figured out the key syntax differences (GitHub Copilot for the win!), it ended up being much easier than I expected once I stopped doing it manually and automated the boring parts (GitHub Copilot for the win x2!).

If this helped you, feel free to share it with your team so everyone can standardize MCP config faster. And maybe give a little GitHub Star on the repo, so I know you like it ;).

Cheers!!

/Peter