tsconfig with paths and include fails

app+myapp.ts

export class MyApp {
	execute() {
		return true;
	}
}

test+mytest.ts

import { MyApp } from "@app/myapp";

export function run() {
	let app = new MyApp();
	console.assert(app.execute());
}

test.max.js

define("app/myapp", ["require", "exports"], function (require, exports) {
    "use strict";
    Object.defineProperty(exports, "__esModule", { value: true });
    var MyApp = /** @class */ (function () {
        function MyApp() {
        }
        MyApp.prototype.execute = function () {
            return true;
        };
        return MyApp;
    }());
    exports.MyApp = MyApp;
});
define("test/mytest", ["require", "exports", "app/myapp"], function (require, exports, myapp_1) {
    "use strict";
    Object.defineProperty(exports, "__esModule", { value: true });
    function run() {
        var app = new myapp_1.MyApp();
        console.assert(app.execute());
    }
    exports.run = run;
});

tsconfig-test.json

{
	"extends": "./tsconfig",
	"compilerOptions": {
		"outFile": "./built/test.max.js"
	},
	"include": ["test/**/*.ts"]
}

tsconfig.json

{
	"compilerOptions": {
		"declaration": false,
		"module": "amd",
		"target": "es5",
		"noImplicitAny": true,
		"sourceMap": false,
		"outFile": "./built/app.max.js",
		"moduleResolution": "node",
		"baseUrl": "./",
		"paths": {
			"@app/*": ["./app/*"]
		}
	}
	//"include": ["app/**/*.ts"]
}

Relates to microsoft/vscode#59116