diff --git a/SConstruct b/SConstruct
index 85f76000b710..a056a0c3ae72 100644
--- a/SConstruct
+++ b/SConstruct
@@ -157,7 +157,6 @@ opts.Add(BoolVariable('deprecated', "Enable deprecated features", True))
 opts.Add(BoolVariable('gdscript', "Enable GDScript support", True))
 opts.Add(BoolVariable('minizip', "Enable ZIP archive support using minizip", True))
 opts.Add(BoolVariable('xaudio2', "Enable the XAudio2 audio driver", False))
-opts.Add(BoolVariable('xml', "Enable XML format support for resources", True))
 
 # Advanced options
 opts.Add(BoolVariable('disable_3d', "Disable 3D nodes for a smaller executable", False))
@@ -228,14 +227,14 @@ Help(opts.GenerateHelpText(env_base))  # generate help
 
 # add default include paths
 
-env_base.Append(CPPPATH=['#editor', '#drivers', '#'])
+env_base.Append(CPPPATH=['#editor', '#'])
 
 # configure ENV for platform
 env_base.platform_exporters = platform_exporters
 env_base.platform_apis = platform_apis
 
 if (env_base['target'] == 'debug'):
-    env_base.Append(CPPDEFINES=['DEBUG_MEMORY_ALLOC', 'SCI_NAMESPACE'])
+    env_base.Append(CPPDEFINES=['DEBUG_MEMORY_ALLOC'])
 
 if (env_base['no_editor_splash']):
     env_base.Append(CPPDEFINES=['NO_EDITOR_SPLASH'])
@@ -444,8 +443,6 @@ if selected_platform in platform_list:
             env.Append(CPPDEFINES=['ADVANCED_GUI_DISABLED'])
     if env['minizip']:
         env.Append(CPPDEFINES=['MINIZIP_ENABLED'])
-    if env['xml']:
-        env.Append(CPPDEFINES=['XML_ENABLED'])
 
     if not env['verbose']:
         methods.no_verbose(sys, env)
diff --git a/drivers/gles2/rasterizer_gles2.cpp b/drivers/gles2/rasterizer_gles2.cpp
index bd03bd71f676..1dd594cc20ea 100644
--- a/drivers/gles2/rasterizer_gles2.cpp
+++ b/drivers/gles2/rasterizer_gles2.cpp
@@ -32,7 +32,7 @@
 
 #include "core/os/os.h"
 #include "core/project_settings.h"
-#include "gl_context/context_gl.h"
+#include "drivers/gl_context/context_gl.h"
 
 #define _EXT_DEBUG_OUTPUT_SYNCHRONOUS_ARB 0x8242
 #define _EXT_DEBUG_NEXT_LOGGED_MESSAGE_LENGTH_ARB 0x8243
diff --git a/drivers/gles3/rasterizer_gles3.cpp b/drivers/gles3/rasterizer_gles3.cpp
index d3f6dcd49736..6f13df621f0d 100644
--- a/drivers/gles3/rasterizer_gles3.cpp
+++ b/drivers/gles3/rasterizer_gles3.cpp
@@ -32,7 +32,7 @@
 
 #include "core/os/os.h"
 #include "core/project_settings.h"
-#include "gl_context/context_gl.h"
+#include "drivers/gl_context/context_gl.h"
 
 RasterizerStorage *RasterizerGLES3::get_storage() {
 
diff --git a/drivers/png/SCsub b/drivers/png/SCsub
index 986c36c67c57..22fb1817d12b 100644
--- a/drivers/png/SCsub
+++ b/drivers/png/SCsub
@@ -27,6 +27,8 @@ if env['builtin_libpng']:
     thirdparty_sources = [thirdparty_dir + file for file in thirdparty_sources]
 
     env_png.Append(CPPPATH=[thirdparty_dir])
+    # Needed for drivers includes and in platform/javascript
+    env.Append(CPPPATH=[thirdparty_dir])
 
     # Currently .ASM filter_neon.S does not compile on NT.
     import os
diff --git a/drivers/register_driver_types.cpp b/drivers/register_driver_types.cpp
index c6d36a5749f7..9f5d9c1abf56 100644
--- a/drivers/register_driver_types.cpp
+++ b/drivers/register_driver_types.cpp
@@ -31,11 +31,11 @@
 #include "register_driver_types.h"
 
 #include "core/math/geometry.h"
-#include "png/image_loader_png.h"
-#include "png/resource_saver_png.h"
+#include "drivers/png/image_loader_png.h"
+#include "drivers/png/resource_saver_png.h"
 
 #ifdef TOOLS_ENABLED
-#include "convex_decomp/b2d_decompose.h"
+#include "drivers/convex_decomp/b2d_decompose.h"
 #endif
 
 #ifdef TOOLS_ENABLED
diff --git a/editor/SCsub b/editor/SCsub
index d5ac8c700807..82a4ecb6c075 100644
--- a/editor/SCsub
+++ b/editor/SCsub
@@ -79,7 +79,9 @@ if env['tools']:
     env.CommandNoCache('#editor/builtin_fonts.gen.h', flist, run_in_subprocess(editor_builders.make_fonts_header))
 
     env.add_source_files(env.editor_sources, "*.cpp")
-    env.add_source_files(env.editor_sources, ["#thirdparty/misc/clipper.cpp"])
+    env_thirdparty = env.Clone()
+    env_thirdparty.disable_warnings()
+    env_thirdparty.add_source_files(env.editor_sources, ["#thirdparty/misc/clipper.cpp"])
 
     SConscript('collada/SCsub')
     SConscript('doc/SCsub')
diff --git a/modules/freetype/SCsub b/modules/freetype/SCsub
index d2f0ad042a99..7ca40c1b8b26 100644
--- a/modules/freetype/SCsub
+++ b/modules/freetype/SCsub
@@ -1,9 +1,11 @@
 #!/usr/bin/env python
 
 Import('env')
+Import('env_modules')
+
 from compat import isbasestring
 
-# Not building in a separate env as scene needs it
+env_freetype = env_modules.Clone()
 
 # Thirdparty source files
 if env['builtin_freetype']:
@@ -54,28 +56,33 @@ if env['builtin_freetype']:
     ]
     thirdparty_sources = [thirdparty_dir + file for file in thirdparty_sources]
 
+    if env['platform'] == 'uwp':
+        # Include header for UWP to fix build issues
+        env_freetype.Append(CCFLAGS=['/FI', '"modules/freetype/uwpdef.h"'])
+
     sfnt = thirdparty_dir + 'src/sfnt/sfnt.c'
-
-    if 'platform' in env:
-        if env['platform'] == 'uwp':
-            # Include header for UWP to fix build issues
-            env.Append(CCFLAGS=['/FI', '"modules/freetype/uwpdef.h"'])
-        elif env['platform'] == 'javascript':
-            # Forcibly undefine this macro so SIMD is not used in this file,
-            # since currently unsupported in WASM
-            sfnt = env.Object(sfnt, CPPFLAGS=['-U__OPTIMIZE__'])
-
+    if env['platform'] == 'javascript':
+        # Forcibly undefine this macro so SIMD is not used in this file,
+        # since currently unsupported in WASM
+        sfnt = env_freetype.Object(sfnt, CPPFLAGS=['-U__OPTIMIZE__'])
     thirdparty_sources += [sfnt]
 
-    env.Append(CPPPATH=[thirdparty_dir, thirdparty_dir + "/include"])
+    env_freetype.Append(CPPPATH=[thirdparty_dir + "/include"])
+    # Also needed in main env for scene/
+    env.Append(CPPPATH=[thirdparty_dir + "/include"])
 
-    # also requires libpng headers
+    env_freetype.Append(CCFLAGS=['-DFT2_BUILD_LIBRARY', '-DFT_CONFIG_OPTION_USE_PNG'])
+    if (env['target'] != 'release'):
+        env_freetype.Append(CCFLAGS=['-DZLIB_DEBUG'])
+
+    # Also requires libpng headers
     if env['builtin_libpng']:
-        env.Append(CPPPATH=["#thirdparty/libpng"])
+        env_freetype.Append(CPPPATH=["#thirdparty/libpng"])
+
+    env_thirdparty = env_freetype.Clone()
+    env_thirdparty.disable_warnings()
+    lib = env_thirdparty.add_library("freetype_builtin", thirdparty_sources)
 
-    # FIXME: Find a way to build this in a separate env nevertheless
-    # so that we can disable warnings on thirdparty code
-    lib = env.add_library("freetype_builtin", thirdparty_sources)
     # Needs to be appended to arrive after libscene in the linker call,
     # but we don't want it to arrive *after* system libs, so manual hack
     # LIBS contains first SCons Library objects ("SCons.Node.FS.File object")
@@ -88,12 +95,8 @@ if env['builtin_freetype']:
             break
     if not inserted:
         env.Append(LIBS=[lib])
-    env.Append(CCFLAGS=['-DFT2_BUILD_LIBRARY'])
-    if (env['target'] != 'release'):
-        env.Append(CCFLAGS=['-DZLIB_DEBUG'])
 
 # Godot source files
-env.add_source_files(env.modules_sources, "*.cpp")
-env.Append(CCFLAGS=['-DFREETYPE_ENABLED', '-DFT_CONFIG_OPTION_USE_PNG'])
-
-Export('env')
+env_freetype.add_source_files(env.modules_sources, "*.cpp")
+# Used in scene/, needs to be in main env
+env.Append(CCFLAGS=['-DFREETYPE_ENABLED'])
diff --git a/modules/svg/SCsub b/modules/svg/SCsub
index d14191056f39..22f0b1e3eb74 100644
--- a/modules/svg/SCsub
+++ b/modules/svg/SCsub
@@ -1,6 +1,9 @@
 #!/usr/bin/env python
 
 Import('env')
+Import('env_modules')
+
+env_svg = env_modules.Clone()
 
 # Thirdparty source files
 thirdparty_dir = "#thirdparty/nanosvg/"
@@ -9,12 +12,15 @@ thirdparty_sources = [
 ]
 thirdparty_sources = [thirdparty_dir + file for file in thirdparty_sources]
 
+env_svg.Append(CPPPATH=[thirdparty_dir])
+# FIXME: Needed in editor/editor_themes.cpp for now, but ideally there
+# shouldn't be a dependency on modules/ and its own 3rd party deps.
 env.Append(CPPPATH=[thirdparty_dir])
 env.Append(CCFLAGS=["-DSVG_ENABLED"])
 
-env_thirdparty = env.Clone()
+env_thirdparty = env_svg.Clone()
 env_thirdparty.disable_warnings()
 env_thirdparty.add_source_files(env.modules_sources, thirdparty_sources)
 
 # Godot's own source files
-env.add_source_files(env.modules_sources, "*.cpp")
+env_svg.add_source_files(env.modules_sources, "*.cpp")
diff --git a/platform/haiku/detect.py b/platform/haiku/detect.py
index 7ecdd2bb11b6..8d704ac65700 100644
--- a/platform/haiku/detect.py
+++ b/platform/haiku/detect.py
@@ -148,7 +148,7 @@ def configure(env):
     ## Flags
 
     env.Append(CPPPATH=['#platform/haiku'])
-    env.Append(CPPFLAGS=['-DUNIX_ENABLED', '-DOPENGL_ENABLED', '-DGLES_ENABLED', '-DGLES_OVER_GL'])
+    env.Append(CPPFLAGS=['-DUNIX_ENABLED', '-DOPENGL_ENABLED', '-DGLES_ENABLED'])
     env.Append(CPPFLAGS=['-DMEDIA_KIT_ENABLED'])
     # env.Append(CCFLAGS=['-DFREETYPE_ENABLED'])
     env.Append(CPPFLAGS=['-DPTHREAD_NO_RENAME'])  # TODO: enable when we have pthread_setname_np
diff --git a/platform/haiku/platform_config.h b/platform/haiku/platform_config.h
index 72c8ee2535e7..b00510f5a12d 100644
--- a/platform/haiku/platform_config.h
+++ b/platform/haiku/platform_config.h
@@ -33,5 +33,5 @@
 // for ifaddrs.h needed in drivers/unix/ip_unix.cpp
 #define _BSD_SOURCE 1
 
-#define GLES3_INCLUDE_H "glad/glad.h"
-#define GLES2_INCLUDE_H "glad/glad.h"
+#define GLES3_INCLUDE_H "thirdparty/glad/glad/glad.h"
+#define GLES2_INCLUDE_H "thirdparty/glad/glad/glad.h"
diff --git a/platform/osx/platform_config.h b/platform/osx/platform_config.h
index 3f72831d775d..1d32d5b5b932 100644
--- a/platform/osx/platform_config.h
+++ b/platform/osx/platform_config.h
@@ -30,6 +30,6 @@
 
 #include <alloca.h>
 
-#define GLES3_INCLUDE_H "glad/glad.h"
-#define GLES2_INCLUDE_H "glad/glad.h"
+#define GLES3_INCLUDE_H "thirdparty/glad/glad/glad.h"
+#define GLES2_INCLUDE_H "thirdparty/glad/glad/glad.h"
 #define PTHREAD_RENAME_SELF
diff --git a/platform/windows/platform_config.h b/platform/windows/platform_config.h
index d100385e80a9..aa020ed47094 100644
--- a/platform/windows/platform_config.h
+++ b/platform/windows/platform_config.h
@@ -32,5 +32,5 @@
 //#else
 //#include <alloca.h>
 //#endif
-#define GLES3_INCLUDE_H "glad/glad.h"
-#define GLES2_INCLUDE_H "glad/glad.h"
+#define GLES3_INCLUDE_H "thirdparty/glad/glad/glad.h"
+#define GLES2_INCLUDE_H "thirdparty/glad/glad/glad.h"
diff --git a/platform/x11/detect.py b/platform/x11/detect.py
index 905546e7244f..ee59e9b5a170 100644
--- a/platform/x11/detect.py
+++ b/platform/x11/detect.py
@@ -250,7 +250,8 @@ def configure(env):
     if (os.system("pkg-config --exists alsa") == 0): # 0 means found
         print("Enabling ALSA")
         env.Append(CPPFLAGS=["-DALSA_ENABLED", "-DALSAMIDI_ENABLED"])
-        env.ParseConfig('pkg-config alsa --cflags --libs')
+	# Don't parse --cflags, we don't need to add /usr/include/alsa to include path
+        env.ParseConfig('pkg-config alsa --libs')
     else:
         print("ALSA libraries not found, disabling driver")
 
@@ -278,7 +279,7 @@ def configure(env):
         env.ParseConfig('pkg-config zlib --cflags --libs')
 
     env.Append(CPPPATH=['#platform/x11'])
-    env.Append(CPPFLAGS=['-DX11_ENABLED', '-DUNIX_ENABLED', '-DOPENGL_ENABLED', '-DGLES_ENABLED', '-DGLES_OVER_GL'])
+    env.Append(CPPFLAGS=['-DX11_ENABLED', '-DUNIX_ENABLED', '-DOPENGL_ENABLED', '-DGLES_ENABLED'])
     env.Append(LIBS=['GL', 'pthread'])
 
     if (platform.system() == "Linux"):
diff --git a/platform/x11/platform_config.h b/platform/x11/platform_config.h
index b757be49c313..f6d7f5a8cdd3 100644
--- a/platform/x11/platform_config.h
+++ b/platform/x11/platform_config.h
@@ -36,5 +36,5 @@
 #define PTHREAD_BSD_SET_NAME
 #endif
 
-#define GLES3_INCLUDE_H "glad/glad.h"
-#define GLES2_INCLUDE_H "glad/glad.h"
+#define GLES3_INCLUDE_H "thirdparty/glad/glad/glad.h"
+#define GLES2_INCLUDE_H "thirdparty/glad/glad/glad.h"