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

Source/modules/modules.gypi

 {
   'variables': {
     # Experimental hooks for embedder to provide extra IDL and source files.
     #
     # Note: this is not a supported API. If you rely on this, you will be broken
     # from time to time as the code generator changes in backward incompatible
     # ways.
     'extra_blink_module_idl_files': [],
     'extra_blink_module_files': [],
     # Files for which bindings (.cpp and .h files) will be generated
@@ skipping 246 matching lines @@
       'speech/SpeechRecognitionEvent.idl',
       'speech/SpeechSynthesisEvent.idl',
       'webaudio/AudioProcessingEvent.idl',
       'webaudio/OfflineAudioCompletionEvent.idl',
       'webmidi/MIDIConnectionEvent.idl',
       'webmidi/MIDIMessageEvent.idl',
       'websockets/CloseEvent.idl',
     ],
     'generated_modules_files': [
       # .cpp files from make_modules_generated actions.
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventModules.cpp',
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventModulesHeaders.h',
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventModulesInterfaces.h',
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventModulesNames.cpp',
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventModulesNames.h',
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventTargetModulesHeaders.h',
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventTargetModulesInterfaces.h',
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventTargetModulesNames.cpp',
-      '<(SHARED_INTERMEDIATE_DIR)/blink/EventTargetModulesNames.h',
+      '<(modules_output_dir)/EventModules.cpp',
+      '<(modules_output_dir)/EventModulesHeaders.h',
+      '<(modules_output_dir)/EventModulesInterfaces.h',
+      '<(modules_output_dir)/EventModulesNames.cpp',
+      '<(modules_output_dir)/EventModulesNames.h',
+      '<(modules_output_dir)/EventTargetModulesHeaders.h',
+      '<(modules_output_dir)/EventTargetModulesInterfaces.h',
+      '<(modules_output_dir)/EventTargetModulesNames.cpp',
+      '<(modules_output_dir)/EventTargetModulesNames.h',
     ],
     'modules_files': [
       '<@(extra_blink_module_files)',
       '<@(generated_modules_files)',
       'InitModules.cpp',
       'InitModules.h',
       'battery/BatteryDispatcher.cpp',
       'battery/BatteryDispatcher.h',
       'battery/BatteryManager.cpp',
       'battery/BatteryManager.h',
@@ skipping 676 matching lines @@
       'indexeddb/IDBRequestTest.cpp',
       'indexeddb/IDBTransactionTest.cpp',
       'websockets/WebSocketDeflaterTest.cpp',
       'websockets/WebSocketExtensionDispatcherTest.cpp',
       'websockets/WebSocketExtensionParserTest.cpp',
       'websockets/WebSocketPerMessageDeflateTest.cpp',
       'websockets/WebSocketTest.cpp',
     ],
   },
 }