Varun Vemulapalli

Day 59 of 100 · Phase 7: GitHub Copilot

Custom instructions and MCP servers in Copilot

2 min readBy Varun Vemulapalli

Every time you open a chat, Copilot meets your project for the first time.

Unless you leave it a note. Today: the note, and the plug-ins.

Video explainer · 1:43
Key takeaway

An instructions file tells Copilot your project's rules, and MCP servers give it new tools.

Day 59 visual: Custom instructions and MCP servers in Copilot
The visual from the original post.

The concept

Custom instructions: a Markdown file in your repository that Copilot reads automatically, so you don't repeat rules in every prompt. A system prompt (Day 24) for your project.

The main files, per GitHub and VS Code docs:

  • .github/copilot-instructions.md: rules for the whole repo.
  • .github/instructions/NAME.instructions.md: rules for certain files, e.g. tests.
  • AGENTS.md: a shared format that Copilot and other coding agents can read.

MCP server (Day 38): a connector that gives Copilot new tools, like reading GitHub issues.

Walkthrough: a clinic appointment app

Part 1. Create .github/copilot-instructions.md:

Clinic appointment booking app in Python.

  • Store times in UTC; show clinic local time.
  • Slots are 15 minutes, 08:00–18:00, Mon–Fri.
  • Never log patient names, phones or dates of birth.
  • Every new function needs a test.
  • Plain error messages, e.g. "That slot is taken."

Now ask Chat: "Add a function to cancel an appointment." Without the file, it might log the patient's name. With it, Copilot should follow the clinic's rules and add a test. Check that it did.

Part 2. The GitHub MCP server lets Copilot work with your issues and pull requests. It's available on every plan.
1. In VS Code Extensions, search @mcp github.
2. Select the GitHub MCP server, click Install, confirm you trust it.
3. Sign in with GitHub and approve what it may access.
4. In Chat (Agent), ask: "List open issues in this repo labelled bug."
5. Expand the tool call to confirm the answer came from the server.

Where you see it at work

  • Healthcare: "never log patient data", written once, applied every time.
  • Banking: rounding and currency conventions.
  • Insurance: naming rules for policy and claim fields.
  • Retail: an MCP server for the product catalogue.
  • Product and BA: the instructions file is a living spec you can review.

Install only MCP servers you trust: they act with the access you grant.

Try it today (10–15 min)

1. In any repo, create .github/copilot-instructions.md with 3–5 rules.
2. Ask Chat for a change; does it follow them?
3. Install the GitHub MCP server and ask about your issues.
4. Docs: https://docs.github.com/en/copilot/concepts/prompting-and-context/custom-instructions and https://code.visualstudio.com/docs/agent-customization/mcp-servers

In one sentence

An instructions file tells Copilot your project's rules, and MCP servers give it new tools.

What's the first rule you'd put in your team's instructions file? 👇