Adding a not explicit source makes it explicit.

pkg/analyzer/test/src/context/context_test.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.
 
 library test.src.context.context_test;
 
 import 'dart:async';
 
 import 'package:analyzer/file_system/memory_file_system.dart';
 import 'package:analyzer/src/cancelable_future.dart';
@@ skipping 132 matching lines @@
     ChangeSet changeSet = new ChangeSet();
     changeSet.addedSource(source);
     context.applyChanges(changeSet);
     expect(context.sourcesNeedingProcessing, contains(source));
     return pumpEventQueue().then((_) {
       listener.assertEvent(wereSourcesAdded: true);
       listener.assertNoMoreEvents();
     });
   }
 
+  void test_applyChanges_add_makesExplicit() {
+    Source source = newSource('/test.dart');
+    // get the entry, it's not explicit
+    CacheEntry entry = context.getCacheEntry(source);
+    expect(entry.explicitlyAdded, isFalse);
+    // add the source
+    ChangeSet changeSet = new ChangeSet();
+    changeSet.addedSource(source);
+    context.applyChanges(changeSet);
+    // now the entry is explicit
+    expect(entry.explicitlyAdded, isTrue);
+  }
+
   Future test_applyChanges_change() {
     SourcesChangedListener listener = new SourcesChangedListener();
     context.onSourcesChanged.listen(listener.onData);
     expect(context.sourcesNeedingProcessing, isEmpty);
     Source source = newSource('/test.dart');
     ChangeSet changeSet1 = new ChangeSet();
     changeSet1.addedSource(source);
     context.applyChanges(changeSet1);
     expect(context.sourcesNeedingProcessing, contains(source));
     Source source2 = newSource('/test2.dart');
@@ skipping 2464 matching lines @@
   }
 }
 
 class _AnalysisContextImplTest_test_applyChanges_removeContainer
     implements SourceContainer {
   Source libB;
   _AnalysisContextImplTest_test_applyChanges_removeContainer(this.libB);
   @override
   bool contains(Source source) => source == libB;
 }