Remove several references to JavaFile

pkg/analyzer/lib/src/generated/source_io.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 analyzer.src.generated.source_io;
 
 import 'dart:collection';
 
 import 'package:analyzer/src/generated/engine.dart';
 import 'package:analyzer/src/generated/java_core.dart';
 import 'package:analyzer/src/generated/java_engine.dart';
 import 'package:analyzer/src/generated/java_io.dart';
 import 'package:analyzer/src/generated/source.dart';
 
 export 'package:analyzer/src/generated/source.dart';
 
 /**
  * Instances of the class [DirectoryBasedSourceContainer] represent a source container that
  * contains all sources within a given directory.
  */
+@deprecated
 class DirectoryBasedSourceContainer implements SourceContainer {
   /**
    * The container's path (not `null`).
    */
   String _path;
 
   /**
    * Construct a container representing the specified directory and containing any sources whose
    * [Source.fullName] starts with the directory's path. This is a convenience method,
    * fully equivalent to [DirectoryBasedSourceContainer.con2].
@@ skipping 537 matching lines @@
   }
 
   /**
    * Return `true` if the given URI is a `file` URI.
    *
    * @param uri the URI being tested
    * @return `true` if the given URI is a `file` URI
    */
   static bool isFileUri(Uri uri) => uri.scheme == FILE_SCHEME;
 }