Support per-tool filtering for MCP servers

Currently, when an MCP server is enabled, all tools it exposes are loaded into the system prompt. There is no way to selectively include or exclude individual tools from a server.

Each tool definition consumes context window tokens. For MCP servers that expose many tools (10+), this becomes significant overhead when only one or two tools are actually needed.

It would be helpful to support tool filtering in .mcp.json or .claude/settings.json, for example:

{
    "mcpServers": {
        "my-server": {
            "command": "php",
            "args": ["artisan", "boost:mcp"],
            "allowedTools": ["search-docs"]
        }
    }
}

or via settings:

{
    "mcpToolFilter": {
        "my-server": {
            "only": ["search-docs"]
        }
    }
}

This would keep the server connection active but only register the specified tools, reducing system prompt size and context window usage.