Android's native_tests.gyp should take WebKit's directory structure into account.

build/apk_test.gypi

 # Copyright (c) 2012 The Chromium Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 
 # This file is meant to be included into a target to provide a rule
 # to build APK based test suites.
 #
 # To use this, create a gyp target with the following form:
 # {
 #   'target_name': 'test_suite_name_apk',
@@ skipping 43 matching lines @@
               '--ant-args',
               '-DANDROID_SDK=<(android_sdk)',
               '--ant-args',
               '-DANDROID_SDK_ROOT=<(android_sdk_root)',
               '--ant-args',
               '-DANDROID_SDK_TOOLS=<(android_sdk_tools)',
               '--ant-args',
               '-DANDROID_SDK_VERSION=<(android_sdk_version)',
               '--ant-args',
               '-DANDROID_TOOLCHAIN=<(android_toolchain)',
+              '--ant-args',
+              '-DCHROMIUM_SRC=<(ant_build_out)/../..',
               '--ant-compile'
             ],
           }],
         }],  # 'OS == "android" and gtest_target_type == "shared_library"
       ],  # conditions
     }],
   ],  # target_conditions
 }