Use the package_resolver package.

lib/src/util/dart.dart

 // Copyright (c) 2015, the Dart project authors.  Please see the AUTHORS file
 // for details. All rights reserved. Use of this source code is governed by a
 // BSD-style license that can be found in the LICENSE file.
 
 import 'dart:async';
 import 'dart:isolate';
 
 import 'package:analyzer/analyzer.dart';
 import 'package:source_span/source_span.dart';
 
 import 'string_literal_iterator.dart';
 
 /// Runs [code] in an isolate.
 ///
 /// [code] should be the contents of a Dart entrypoint. It may contain imports;
 /// they will be resolved in the same context as the host isolate. [message] is
 /// passed to the [main] method of the code being run; the caller is responsible
 /// for using this to establish communication with the isolate.
-///
-/// [packageRoot] controls the package root of the isolate. It may be either a
-/// [String] or a [Uri].
-Future<Isolate> runInIsolate(String code, message, {packageRoot,
-    bool checked}) async {
-  if (packageRoot is String) packageRoot = Uri.parse(packageRoot);
-
+Future<Isolate> runInIsolate(String code, message, {bool checked}) async {
   return await Isolate.spawnUri(
       Uri.parse('data:application/dart;charset=utf-8,' + Uri.encodeFull(code)),
       [],
       message,
-      packageRoot: packageRoot,
+      packageRoot: await Isolate.packageRoot,
+      packageConfig: await Isolate.packageConfig,
       checked: checked);
 }
 
 // TODO(nweiz): Move this into the analyzer once it starts using SourceSpan
 // (issue 22977).
 /// Takes a span whose source is the value of a string that has been parsed from
 /// a Dart file and returns the corresponding span from within that Dart file.
 ///
 /// For example, suppose a Dart file contains `@Eval("1 + a")`. The
 /// [StringLiteral] `"1 + a"` is extracted; this is [context]. Its contents are
@@ skipping 26 matching lines @@
   }
 
   var start = contextRunes.offset;
   for (var spanRune in span.text.runes) {
     if (spanRune != contextRunes.current) return null;
     contextRunes.moveNext();
   }
 
   return file.span(start, contextRunes.offset);
 }