diff --git a/Tools/ardupilotwaf/gbenchmark.py b/Tools/ardupilotwaf/gbenchmark.py
index e13f47ff75..9ce2ee1b00 100644
--- a/Tools/ardupilotwaf/gbenchmark.py
+++ b/Tools/ardupilotwaf/gbenchmark.py
@@ -49,13 +49,6 @@ def configure(cfg):
         )
         return
 
-    cfg.start_msg('Checking for gbenchmark submodule')
-    cmake_lists = cfg.srcnode.find_resource('modules/gbenchmark/CMakeLists.txt')
-    if not cmake_lists:
-        cfg.end_msg('not initialized', color='YELLOW')
-        return
-    cfg.end_msg('yes')
-
     cfg.find_program('cmake', mandatory=False)
 
     if not env.CMAKE:
@@ -74,25 +67,18 @@ def configure(cfg):
     bldnode = cfg.bldnode.make_node(cfg.variant)
     prefix_node = bldnode.make_node('gbenchmark')
     my_build_node = bldnode.make_node('gbenchmark_build')
-    my_src_node = cfg.srcnode.find_dir('modules/gbenchmark')
+    my_src_node = cfg.srcnode.make_node('modules/gbenchmark')
 
     env.GBENCHMARK_PREFIX_REL = prefix_node.path_from(bldnode)
     env.GBENCHMARK_BUILD = my_build_node.abspath()
     env.GBENCHMARK_BUILD_REL = my_build_node.path_from(bldnode)
     env.GBENCHMARK_SRC = my_src_node.abspath()
 
-    cfg.start_msg('Configuring gbenchmark')
-    try:
-        _configure_cmake(cfg, bldnode)
-        cfg.end_msg('done')
-    except:
-        cfg.end_msg('failed', color='YELLOW')
-        return
-
     env.INCLUDES_GBENCHMARK = [prefix_node.make_node('include').abspath()]
     env.LIBPATH_GBENCHMARK = [prefix_node.make_node('lib').abspath()]
     env.LIB_GBENCHMARK = ['benchmark']
 
+    env.append_value('GIT_SUBMODULES', 'gbenchmark')
     env.HAS_GBENCHMARK = True
 
 class gbenchmark_build(Task.Task):
@@ -116,10 +102,6 @@ class gbenchmark_build(Task.Task):
         bld = self.generator.bld
         cmds = []
 
-        cmake_lists = bld.srcnode.find_resource('modules/gbenchmark/CMakeLists.txt')
-        if not cmake_lists:
-            bld.fatal('Submodule gbenchmark not initialized, please run configure again')
-
         try:
             # Generate build system first, if necessary
             my_build_node = bld.bldnode.find_dir(self.env.GBENCHMARK_BUILD_REL)
diff --git a/Tools/ardupilotwaf/gtest.py b/Tools/ardupilotwaf/gtest.py
index bf4b91372a..58ed9ebc22 100644
--- a/Tools/ardupilotwaf/gtest.py
+++ b/Tools/ardupilotwaf/gtest.py
@@ -20,13 +20,7 @@ def configure(cfg):
         )
         return
 
-    cfg.start_msg('Checking for gtest submodule')
-    readme = cfg.srcnode.find_resource('modules/gtest/README')
-    if not readme:
-        cfg.end_msg('not initialized', color='YELLOW')
-        return
-    cfg.end_msg('yes')
-
+    cfg.env.append_value('GIT_SUBMODULES', 'gtest')
     cfg.env.HAS_GTEST = True
 
 @conf
diff --git a/Tools/ardupilotwaf/mavgen.py b/Tools/ardupilotwaf/mavgen.py
index c00b68e3e5..72cc65e31e 100644
--- a/Tools/ardupilotwaf/mavgen.py
+++ b/Tools/ardupilotwaf/mavgen.py
@@ -53,11 +53,5 @@ def configure(cfg):
 
     env = cfg.env
 
-    cfg.start_msg('Checking for mavgen')
-    if not cfg.srcnode.find_resource('modules/mavlink/pymavlink/tools/mavgen.py'):
-        cfg.fatal('not found, please run: git submodule init && git submodule update')
-        return
-    cfg.end_msg('yes')
-
-    env.MAVLINK_DIR = cfg.srcnode.find_dir('modules/mavlink/').abspath()
+    env.MAVLINK_DIR = cfg.srcnode.make_node('modules/mavlink/').abspath()
     env.MAVGEN = env.MAVLINK_DIR  + '/pymavlink/tools/mavgen.py'
diff --git a/wscript b/wscript
index 61c7152b46..aa0abf4001 100644
--- a/wscript
+++ b/wscript
@@ -97,6 +97,8 @@ def configure(cfg):
     else:
         cfg.end_msg('disabled', color='YELLOW')
 
+    cfg.env.append_value('GIT_SUBMODULES', 'mavlink')
+
     cfg.env.prepend_value('INCLUDES', [
         cfg.srcnode.abspath() + '/libraries/',
     ])