Add support for repo-specific / folder-specific MCP configs

[rishitank]

Describe the feature or problem you'd like to solve

I want to be able to support sourcing the MCP configuration from multiple sources - ideally a global config and a project-specific config. The reason for this is that for some projects I need specific MCP servers e.g. neo4j memory MCP server, whereas for other projects it would not be applicable (or would have a different neo4j MCP server config for example).

Proposed solution

A simple solution would be to provide a repeatable --mcp-config flag that would be able to source a MCP config from multiple places and internally you could concatenate the MCP configuration. This could also work by having the global MCP config in your ~/.copilot directory being loaded automatically, with support for additional source of MCP configurations.

Example prompts or workflows

When starting a new session I would say:
Read your neo4j memory to understand the structure, patterns, rules and features of this codebase, all the previous work that has been implemented so far and all the learnings that have come from it.

Additional context

No response

[kvenkatrajan]

+1 - This would also help open up creating subagents (with specific mcp tools) to operate on specific directories of a repo. Currently we are limited to the set of tools for a given global configuration.

@RyanHecht @skylar-anderson

[ellismg]

I merged in a change to the CLI to add --additional-mcp-config, which allows you to pass either a JSON document or a path to a JSON file.

The --additional-mcp-config flag that allows you to temporarily add or override MCP server configurations for a single CLI session without modifying your ~/.copilot/mcp-config.json file.

You can pass MCP server configuration in two ways:

1. Inline JSON:

copilot --additional-mcp-config '{"mcpServers": {"my-tool": {...}}}'

2. From a file (prefix with @):

copilot --additional-mcp-config @/path/to/config.json

You can also pass the flag multiple times (later values override earlier ones):

copilot --additional-mcp-config @base.json --additional-mcp-config @overrides.json

This should ship in today's release of the CLI (and should be there now if you install the @prerelease tagg). You'll see the new flag in --help.

[kvenkatrajan]

great thank you!