diff --git a/atom/app/uv_task_runner.h b/atom/app/uv_task_runner.h
index a01c23208cce..578024d70486 100644
--- a/atom/app/uv_task_runner.h
+++ b/atom/app/uv_task_runner.h
@@ -10,7 +10,7 @@
 #include "base/callback.h"
 #include "base/location.h"
 #include "base/single_thread_task_runner.h"
-#include "vendor/node/deps/uv/include/uv.h"
+#include "uv.h"  // NOLINT(build/include)
 
 namespace atom {
 
diff --git a/atom/browser/api/event_subscriber.h b/atom/browser/api/event_subscriber.h
index c43108547bed..8e9dcf518d98 100644
--- a/atom/browser/api/event_subscriber.h
+++ b/atom/browser/api/event_subscriber.h
@@ -11,7 +11,7 @@
 #include "atom/common/api/event_emitter_caller.h"
 #include "base/synchronization/lock.h"
 #include "content/public/browser/browser_thread.h"
-#include "native_mate/native_mate/arguments.h"
+#include "native_mate/arguments.h"
 
 namespace mate {
 
diff --git a/atom/browser/javascript_environment.cc b/atom/browser/javascript_environment.cc
index c158759e2de8..a75cd6c39987 100644
--- a/atom/browser/javascript_environment.cc
+++ b/atom/browser/javascript_environment.cc
@@ -15,7 +15,7 @@
 #include "gin/v8_initializer.h"
 
 #include "atom/common/node_includes.h"
-#include "vendor/node/src/tracing/trace_event.h"
+#include "tracing/trace_event.h"
 
 namespace atom {
 
diff --git a/atom/common/api/atom_bindings.h b/atom/common/api/atom_bindings.h
index d46d047de50c..7a49d285fa9d 100644
--- a/atom/common/api/atom_bindings.h
+++ b/atom/common/api/atom_bindings.h
@@ -11,8 +11,8 @@
 #include "base/process/process_metrics.h"
 #include "base/strings/string16.h"
 #include "native_mate/arguments.h"
+#include "uv.h"  // NOLINT(build/include)
 #include "v8/include/v8.h"
-#include "vendor/node/deps/uv/include/uv.h"
 
 namespace node {
 class Environment;
diff --git a/atom/common/atom_command_line.cc b/atom/common/atom_command_line.cc
index 54420b533a6b..287e43f75fef 100644
--- a/atom/common/atom_command_line.cc
+++ b/atom/common/atom_command_line.cc
@@ -5,7 +5,7 @@
 #include "atom/common/atom_command_line.h"
 
 #include "base/command_line.h"
-#include "node/deps/uv/include/uv.h"
+#include "uv.h"  // NOLINT(build/include)
 
 namespace atom {
 
diff --git a/atom/common/crash_reporter/crash_reporter_mac.h b/atom/common/crash_reporter/crash_reporter_mac.h
index 97c7164bb7ab..359875319d6e 100644
--- a/atom/common/crash_reporter/crash_reporter_mac.h
+++ b/atom/common/crash_reporter/crash_reporter_mac.h
@@ -12,8 +12,8 @@
 #include "atom/common/crash_reporter/crash_reporter.h"
 #include "base/compiler_specific.h"
 #include "base/strings/string_piece.h"
-#include "vendor/crashpad/client/crash_report_database.h"
-#include "vendor/crashpad/client/simple_string_dictionary.h"
+#include "crashpad/client/crash_report_database.h"
+#include "crashpad/client/simple_string_dictionary.h"
 
 namespace base {
 template <typename T>
diff --git a/atom/common/crash_reporter/crash_reporter_mac.mm b/atom/common/crash_reporter/crash_reporter_mac.mm
index 6825d03f0b62..636ce4b065fd 100644
--- a/atom/common/crash_reporter/crash_reporter_mac.mm
+++ b/atom/common/crash_reporter/crash_reporter_mac.mm
@@ -14,9 +14,9 @@
 #include "base/strings/stringprintf.h"
 #include "base/strings/sys_string_conversions.h"
 #include "base/threading/thread_restrictions.h"
-#include "vendor/crashpad/client/crashpad_client.h"
-#include "vendor/crashpad/client/crashpad_info.h"
-#include "vendor/crashpad/client/settings.h"
+#include "crashpad/client/crashpad_client.h"
+#include "crashpad/client/crashpad_info.h"
+#include "crashpad/client/settings.h"
 
 namespace crash_reporter {
 
diff --git a/atom/common/node_bindings.h b/atom/common/node_bindings.h
index 00a45b616851..0647d30cfaeb 100644
--- a/atom/common/node_bindings.h
+++ b/atom/common/node_bindings.h
@@ -8,8 +8,8 @@
 #include "base/macros.h"
 #include "base/memory/weak_ptr.h"
 #include "base/single_thread_task_runner.h"
+#include "uv.h"  // NOLINT(build/include)
 #include "v8/include/v8.h"
-#include "vendor/node/deps/uv/include/uv.h"
 
 namespace base {
 class MessageLoop;
diff --git a/atom/common/node_includes.h b/atom/common/node_includes.h
index 19e1ef2670f1..edd4812e01c2 100644
--- a/atom/common/node_includes.h
+++ b/atom/common/node_includes.h
@@ -29,13 +29,13 @@
 #undef LIKELY
 #undef arraysize
 #undef debug_string  // This is defined in macOS 10.9 SDK in AssertMacros.h.
-#include "vendor/node/src/env-inl.h"
-#include "vendor/node/src/env.h"
-#include "vendor/node/src/node.h"
-#include "vendor/node/src/node_buffer.h"
-#include "vendor/node/src/node_debug_options.h"
-#include "vendor/node/src/node_internals.h"
-#include "vendor/node/src/node_platform.h"
+#include "env-inl.h"
+#include "env.h"
+#include "node.h"
+#include "node_buffer.h"
+#include "node_debug_options.h"
+#include "node_internals.h"
+#include "node_platform.h"
 
 namespace node {
 namespace tracing {
diff --git a/atom/renderer/atom_renderer_client.cc b/atom/renderer/atom_renderer_client.cc
index 1ad1df3d878c..9a1245182be8 100644
--- a/atom/renderer/atom_renderer_client.cc
+++ b/atom/renderer/atom_renderer_client.cc
@@ -23,7 +23,7 @@
 
 #include "atom/common/node_includes.h"
 #include "atom_natives.h"  // NOLINT: This file is generated with js2c
-#include "vendor/node/src/tracing/trace_event.h"
+#include "tracing/trace_event.h"
 
 namespace atom {
 
diff --git a/chromium_src/chrome/renderer/media/chrome_key_systems.cc b/chromium_src/chrome/renderer/media/chrome_key_systems.cc
index 5da793ec584f..902e0c71c9b4 100644
--- a/chromium_src/chrome/renderer/media/chrome_key_systems.cc
+++ b/chromium_src/chrome/renderer/media/chrome_key_systems.cc
@@ -20,8 +20,7 @@
 #include "media/base/key_system_properties.h"
 #include "media/media_features.h"
 
-// #include "widevine_cdm_version.h" // In SHARED_INTERMEDIATE_DIR.
-#include "third_party/widevine/cdm/stub/widevine_cdm_version.h"
+#include "widevine_cdm_version.h"  // In SHARED_INTERMEDIATE_DIR.
 
 // The following must be after widevine_cdm_version.h.
 
diff --git a/electron.gyp b/electron.gyp
index 62dfef265ea8..fec9239e480e 100644
--- a/electron.gyp
+++ b/electron.gyp
@@ -304,6 +304,7 @@
         '<(libchromiumcontent_src_dir)/third_party/',
         '<(libchromiumcontent_src_dir)/components/cdm',
         '<(libchromiumcontent_src_dir)/third_party/widevine',
+        '<(libchromiumcontent_src_dir)/third_party/widevine/cdm/stub',
         '<(libchromiumcontent_src_dir)/third_party/protobuf/src',
         # The 'third_party/webrtc/modules/desktop_capture/desktop_capture_options.h' is using 'rtc_base/constructormagic.h'.
         '<(libchromiumcontent_src_dir)/third_party/webrtc',
@@ -584,6 +585,7 @@
           'action': [
             'python',
             'tools/js2c.py',
+            'vendor/node',
             '<@(_outputs)',
             '<(js2c_input_dir)',
           ],
diff --git a/tools/js2c.py b/tools/js2c.py
index 61f490067fe8..ecd39e6c68af 100755
--- a/tools/js2c.py
+++ b/tools/js2c.py
@@ -24,14 +24,15 @@ namespace node {{
 
 
 def main():
-  natives = os.path.abspath(sys.argv[1])
-  js_source_files = glob.glob('{0}/*.js'.format(sys.argv[2]))
+  node_path = os.path.abspath(sys.argv[1])
+  natives = os.path.abspath(sys.argv[2])
+  js_source_files = glob.glob('{0}/*.js'.format(sys.argv[3]))
 
-  call_js2c(natives, js_source_files)
+  call_js2c(node_path, natives, js_source_files)
 
 
-def call_js2c(natives, js_source_files):
-  js2c = os.path.join(SOURCE_ROOT, 'vendor', 'node', 'tools', 'js2c.py')
+def call_js2c(node_path, natives, js_source_files):
+  js2c = os.path.join(node_path, 'tools', 'js2c.py')
   src_dir = os.path.dirname(js_source_files[0])
   with scoped_cwd(src_dir):
     subprocess.check_call(