Document per-repo .mcp.json for Copilot CLI

[loganrosen]

Why:

Closes #44234

The Copilot CLI MCP how-to (add-mcp-servers.md) only documents the user-level ~/.copilot/mcp-config.json and the interactive /mcp add flow. The CLI also reads per-repository configuration from .mcp.json and .github/mcp.json, but neither this how-to nor the "Add an MCP server" section of use-copilot-cli.md mentions those files at all. The relevant trust and prompt-mode behaviours live only in the reference pages and are not linked from the how-to.

This has produced several related bug reports in github/copilot-cli whose root cause is partly documentation — see #44234 for the list.

What's being changed:

Adds a new ### Adding per-repository MCP servers subsection to content/copilot/how-tos/copilot-cli/customize-copilot/add-mcp-servers.md covering:

• The .mcp.json (project root) and .github/mcp.json file locations, with their recommended uses.
• Lookup behaviour: the CLI walks from the current working directory up to the Git repository root, loading every .mcp.json it finds; closer-to-cwd wins on name conflicts; project-level definitions take precedence over ~/.copilot/mcp-config.json.
• A minimal JSON example pointing back at the existing format.
• A note that workspace MCP servers are loaded only after folder trust is confirmed.
• A note that in prompt mode (copilot -p) workspace MCP servers are not loaded by default, and require setting GITHUB_COPILOT_PROMPT_MODE_WORKSPACE_MCP=true. This connects the env var (already in the reference) back to .mcp.json for the first time.
• A clarification that .vscode/mcp.json is not read, pointing to the existing migration recipe.

All claims were verified against Copilot CLI v1.0.44-2 (the bundled JS) and confirmed by running copilot mcp list and copilot -p in both modes.

Check off the following:

• A subject matter expert (SME) has reviewed the technical accuracy of the content in this PR. In most cases, the author can be the SME. Open source contributions may require an SME review from GitHub staff.
• The changes in this PR meet the docs fundamentals that are required for all info.
• All CI checks are passing and the changes look good in a preview environment.
• Documentation accessibility guidelines have been followed.

[github-actions]

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Source	Review	Production	What Changed
copilot/how-tos/copilot-cli/customize-copilot/add-mcp-servers.md	fpt ghec	fpt ghec

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🤖 This comment is automatically generated.

[Copilot]

Pull request overview

Adds documentation to the Copilot CLI MCP how-to explaining how to configure MCP servers per-repository using .mcp.json / .github/mcp.json, including precedence rules and prompt-mode / trust-related behavior.

Changes:

• Documented per-repository MCP configuration file locations (.mcp.json and .github/mcp.json) and precedence over user config.
• Added an example per-repo MCP JSON config and notes about folder trust and prompt mode (copilot -p) behavior.
• Clarified that VS Code’s .vscode/mcp.json is not consumed by Copilot CLI and linked to migration guidance.

[Sharra-writes]

@loganrosen I'll take this to the Copilot team to see if they have any objections.

[granjacours608-ux]

https://github.com/granjacours608-ux?tab=repositories

[ded-furby]

The new section covers the file locations and prompt-mode/trust behavior well, but it still seems to miss one of the issue's concrete requirements: project-level configs can use either the { "mcpServers": { ... } } shape or the bare Claude-style { "name": { ... } } shape. Right now the example and the VS Code note only show the mcpServers form, so readers with an existing bare .mcp.json still won't know that format is valid.

Could you add a brief sentence here (or next to the example) calling out both accepted top-level shapes, and reserve the warning for the unsupported VS Code servers key? That would close the remaining documentation gap from #44234 and should prevent another class of “.mcp.json not loading” reports.