Use Element's source paths instead of URIs as a key in the index.

pkg/analyzer/lib/src/generated/source.dart

 // Copyright (c) 2014, 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.
 
 // This code was auto-generated, is not intended to be edited, and is subject to
 // significant change. Please see the README file for more information.
 
 library engine.source;
 
 import 'dart:collection';
@@ skipping 620 matching lines @@
    * @return the source representing the contained URI
    */
   Source resolveUri(Source containingSource, String containedUri) {
     if (containedUri == null || containedUri.isEmpty) {
       return null;
     }
     try {
       // Force the creation of an escaped URI to deal with spaces, etc.
       return _internalResolveUri(containingSource, parseUriWithException(containedUri));
     } catch (exception, stackTrace) {
+      String containingFullName =
+          containingSource != null ? containingSource.fullName : '<null>';
       AnalysisEngine.instance.logger.logError(
-          "Could not resolve URI ($containedUri) relative to source (${containingSource.fullName})",
+          "Could not resolve URI ($containedUri) relative to source ($containingFullName)",
           new CaughtException(exception, stackTrace));
       return null;
     }
   }
 
   /**
    * Return an absolute URI that represents the given source, or `null` if a valid URI cannot
    * be computed.
    *
    * @param source the source to get URI for
@@ skipping 291 matching lines @@
 
   /**
    * Return an absolute URI that represents the given source, or `null` if a valid URI cannot
    * be computed.
    *
    * @param source the source to get URI for
    * @return the absolute URI representing the given source
    */
   Uri restoreAbsolute(Source source) => null;
 }