Support GitHub Copilot CLI and Desktop

[mishamilovidov]

Problem

DotAgents manages user and project configuration for Claude Code and Codex. It does not manage GitHub Copilot CLI or Desktop.

Copilot uses ~/.copilot/mcp-config.json for user MCP configuration. Projects use .mcp.json, with .github/mcp.json as an existing alternative. Without a Copilot target, users must maintain this configuration separately.

Proposed behavior

• Add a copilot target for user and project scopes.
• Use COPILOT_HOME/mcp-config.json, with ~/.copilot/mcp-config.json as the user fallback.
• Create .mcp.json for projects, but reuse .github/mcp.json when it already exists.
• Preserve unmanaged entries under mcpServers during updates.
• Support stdio and HTTP servers, including environment references.
• Discover native skills under user and project .agents/skills directories.

Acceptance criteria

• Do not rewrite an unchanged MCP file.
• Repair unsafe permissions on the user MCP file without changing its content.
• Create the user MCP file with mode 0600 on POSIX systems.
• Preserve unmanaged MCP entries during install and update operations.
• Add focused tests and user documentation for both scopes.

Implementation

A draft implementation is available in #166.