feat: add file-based MCP server configuration

[Philipp0205]

• Discover and merge MCP servers from mcp.json files at global and project-level locations, aligning with the VS Code / GitHub Copilot CLI convention
• Integrate file-based servers into the existing mcp server configuration with merge (files < preferences < extension points)
• refresh mcp servers when mcp.json files change in the workspace

Closes #127

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