Adding a not explicit source makes it explicit.

pkg/analyzer/lib/src/context/context.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.
 
 library analyzer.src.context.context;
 
 import 'dart:async';
 import 'dart:collection';
 
 import 'package:analyzer/instrumentation/instrumentation.dart';
@@ skipping 1747 matching lines @@
   void _sourceAvailable(Source source) {
     driver.reset();
     // TODO(brianwilkerson) This method needs to check whether the source was
     // previously being implicitly analyzed. If so, the cache entry needs to be
     // update to reflect the new status and an event needs to be generated to
     // inform clients that it is no longer being implicitly analyzed.
     CacheEntry entry = _cache.get(source);
     if (entry == null) {
       _createCacheEntry(source, true);
     } else {
+      entry.explicitlyAdded = true;
       entry.modificationTime = getModificationStamp(source);
       entry.setState(CONTENT, CacheState.INVALID);
     }
   }
 
   /**
    * Invalidate the [source] that was changed and any sources that referenced
    * the source before it existed.
    */
   void _sourceChanged(Source source) {
@@ skipping 356 matching lines @@
     DartSdk sdk = factory.dartSdk;
     if (sdk == null) {
       throw new IllegalArgumentException(
           "The source factory for an SDK analysis context must have a DartUriResolver");
     }
     return new AnalysisCache(<CachePartition>[
       AnalysisEngine.instance.partitionManager_new.forSdk(sdk)
     ]);
   }
 }