Always pass absolute paths to dart2js.

lib/src/dart.dart

 // Copyright (c) 2013, 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.
 
 /// A library for compiling Dart code and manipulating analyzer parse trees.
 library pub.dart;
 
 import 'dart:async';
 import 'dart:io';
 import 'dart:isolate';
@@ skipping 83 matching lines @@
     }
 
     if (environment == null) environment = {};
     if (commandLineOptions != null) options.addAll(commandLineOptions);
 
     if (packageRoot == null) {
       packageRoot = path.join(path.dirname(entrypoint), 'packages');
     }
 
     return compiler.compile(
-        path.toUri(entrypoint),
+        path.toUri(path.absolute(entrypoint)),
         provider.libraryRoot,
-        path.toUri(appendSlash(packageRoot)),
+        path.toUri(appendSlash(path.absolute(packageRoot))),
         provider.provideInput,
         provider.handleDiagnostic,
         options,
         provider.provideOutput,
         environment);
   });
 }
 
 /// Returns whether [dart] looks like an entrypoint file.
 bool isEntrypoint(CompilationUnit dart) {
@@ skipping 98 matching lines @@
   Isolate.spawnUri(Uri.parse(message['uri']), [], message['message'],
           packageRoot: packageRoot)
       .then((_) => replyTo.send({'type': 'success'}))
       .catchError((e, stack) {
     replyTo.send({
       'type': 'error',
       'error': CrossIsolateException.serialize(e, stack)
     });
   });
 }