Separate the generated files from core and modules to their own sub-dirs.

Source/modules/modules.gyp

 #
 # Copyright (C) 2013 Google Inc. All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
 # modification, are permitted provided that the following conditions are
 # met:
 #
 #     * Redistributions of source code must retain the above copyright
 # notice, this list of conditions and the following disclaimer.
 #     * Redistributions in binary form must reproduce the above
@@ skipping 30 matching lines @@
       '<(DEPTH)/third_party/zlib/zlib.gyp:zlib',
       '<(DEPTH)/third_party/sqlite/sqlite.gyp:sqlite',
       '../config.gyp:config',
       '../core/core.gyp:webcore',
       'make_modules_generated',
     ],
     'defines': [
       'BLINK_IMPLEMENTATION=1',
       'INSIDE_BLINK',
     ],
+    'include_dirs': [
+      # FIXME: Remove these once scripts generate qualified
+      # includes correctly: http://crbug.com/380054
+      '<(blink_core_output_dir)',
+      '<(blink_modules_output_dir)',
+    ],
     'sources': [
       '<@(modules_files)',
       '<@(bindings_modules_v8_generated_aggregate_files)',
     ],
     # Disable c4267 warnings until we fix size_t to int truncations.
     'msvs_disabled_warnings': [ 4267, 4334, ]
   },
   {
     'target_name': 'modules_testing',
     'type': 'static_library',
@@ skipping 23 matching lines @@
     ],
     'sources': [
       # bison rule
       '../core/css/CSSGrammar.y',
       '../core/xml/XPathGrammar.y',
     ],
     'actions': [
     ],
   }],
 }