Files are added with absolute URIs, but invalidated with file URIs.

pkg/front_end/test/incremental_kernel_generator_test.dart

 // Copyright (c) 2017, 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 'package:front_end/compiler_options.dart';
 import 'package:front_end/incremental_kernel_generator.dart';
 import 'package:front_end/memory_file_system.dart';
 import 'package:front_end/src/incremental/byte_store.dart';
@@ skipping 464 matching lines @@
 import self as self;
 import "dart:core" as core;
 
 static method main() → dynamic {
   core::double v = 2.3;
 }
 ''');
     }
   }
 
+  test_updatePackageSourceUsingFileUri() async {
+    writeFile('/test/.packages', 'test:lib/');
+    Uri aFileUri = writeFile(
+        '/test/bin/a.dart',
+        r'''
+import 'package:test/b.dart';
+var a = b;
+''');
+    Uri bFileUri = writeFile('/test/lib/b.dart', 'var b = 1;');
+    Uri bPackageUri = Uri.parse('package:test/b.dart');
+
+    // Compute the initial state.
+    {
+      Program program = await getInitialState(aFileUri);
+      Library library = _getLibrary(program, aFileUri);
+      expect(
+          _getLibraryText(library),
+          r'''
+library;
+import self as self;
+import "dart:core" as core;
+import "package:test/b.dart" as b;
+
+static field core::int a = b::b;
+''');
+    }
+
+    // Update b.dart and use file URI to invalidate it.
+    // The delta is recomputed even though b.dart is used with the package URI.
+    writeFile('/test/lib/b.dart', 'var b = 1.2;');
+    incrementalKernelGenerator.invalidate(bFileUri);
+    {
+      DeltaProgram delta = await incrementalKernelGenerator.computeDelta();
+      Program program = delta.newProgram;
+      _assertLibraryUris(program, includes: [aFileUri, bPackageUri]);
+      Library library = _getLibrary(program, aFileUri);
+      expect(
+          _getLibraryText(library),
+          r'''
+library;
+import self as self;
+import "dart:core" as core;
+import "package:test/b.dart" as b;
+
+static field core::double a = b::b;
+''');
+    }
+  }
+
   test_updatePart() async {
     writeFile('/test/.packages', 'test:lib/');
     String libPath = '/test/lib/test.dart';
     String partPath = '/test/lib/bar.dart';
     Uri libUri = writeFile(
         libPath,
         r'''
 library foo;
 part 'bar.dart';
 var a = 1;
@@ skipping 114 matching lines @@
     throw fail('No library found with URI "$uri"');
   }
 
   String _getLibraryText(Library library) {
     StringBuffer buffer = new StringBuffer();
     new Printer(buffer, syntheticNames: new NameSystem())
         .writeLibraryFile(library);
     return buffer.toString();
   }
 }