diff --git a/desmume/configure.ac b/desmume/configure.ac
index 4e628bce2..aa97d7f1b 100644
--- a/desmume/configure.ac
+++ b/desmume/configure.ac
@@ -332,7 +332,6 @@ AC_CONFIG_FILES([Makefile
                  src/gtk/doc/Makefile
                  src/gtk-glade/Makefile
                  src/gtk-glade/doc/Makefile
-                 src/windows/Makefile
 		 src/gdbstub/Makefile
 		 autopackage/default.apspec
 ])
diff --git a/desmume/src/Makefile.am b/desmume/src/Makefile.am
index 43ede26fc..5ee8cf0f7 100644
--- a/desmume/src/Makefile.am
+++ b/desmume/src/Makefile.am
@@ -8,34 +8,37 @@ SUBDIRS = . gdbstub $(UI_DIR)
 else
 SUBDIRS = . $(UI_DIR)
 endif
-DIST_SUBDIRS = . gdbstub cli cocoa gtk gtk-glade windows
+DIST_SUBDIRS = . gdbstub cli cocoa gtk gtk-glade
 noinst_LIBRARIES = libdesmume.a
 libdesmume_a_SOURCES = \
-        armcpu.cpp armcpu.h ARM9.h \
-        arm_instructions.cpp arm_instructions.h \
-        bios.cpp bios.h bits.h cp15.cpp cp15.h \
+	armcpu.cpp armcpu.h \
+	arm_instructions.cpp arm_instructions.h \
+	agg2d.h agg2d.inl \
+	aggdraw.cpp aggdraw.h \
+	bios.cpp bios.h bits.h cp15.cpp cp15.h \
 	commandline.h commandline.cpp \
 	common.cpp common.h \
 	debug.cpp debug.h driver.h \
 	Disassembler.cpp Disassembler.h \
-	dscard.h emufile.h emufile.cpp fat.h FIFO.cpp FIFO.h \
+	emufile.h emufile.cpp fat.h FIFO.cpp FIFO.h \
 	GPU.cpp GPU.h \
 	GPU_osd.cpp GPU_osd.h \
-        mem.h mc.cpp mc.h \
+	mem.h mc.cpp mc.h \
 	path.h \
 	readwrite.cpp readwrite.h \
 	wifi.cpp wifi.h \
-        MMU.cpp MMU.h MMU_timing.h NDSSystem.cpp NDSSystem.h registers.h \
+	mic.h \
+	MMU.cpp MMU.h MMU_timing.h NDSSystem.cpp NDSSystem.h registers.h \
 	OGLRender.cpp OGLRender.h \
 	ROMReader.cpp ROMReader.h \
 	render3D.cpp render3D.h \
 	rtc.cpp rtc.h \
-        saves.cpp saves.h \
-        SPU.cpp SPU.h \
+	saves.cpp saves.h \
+	SPU.cpp SPU.h \
 	matrix.cpp matrix.h \
 	gfx3d.cpp gfx3d.h \
 	texcache.cpp texcache.h \
-        thumb_instructions.cpp thumb_instructions.h types.h \
+	thumb_instructions.cpp thumb_instructions.h types.h \
 	shaders.h \
 	movie.cpp movie.h \
 	PACKED.h PACKED_END.h \
@@ -44,11 +47,11 @@ libdesmume_a_SOURCES = \
 	utils/decrypt/crc.cpp utils/decrypt/crc.h utils/decrypt/decrypt.cpp \
 	utils/decrypt/decrypt.h utils/decrypt/header.cpp utils/decrypt/header.h \
 	utils/task.cpp utils/task.h \
-        addons.cpp addons.h \
+	addons.cpp addons.h \
 	addons/compactFlash.cpp addons/gbagame.cpp addons/none.cpp addons/rumblepak.cpp addons/guitarGrip.cpp addons/expMemory.cpp fs.h \
 	cheatSystem.cpp cheatSystem.h \
 	texcache.cpp texcache.h rasterize.cpp rasterize.h \
-	metaspu/metaspu.cpp \
+	metaspu/metaspu.cpp metaspu/metaspu.h \
 	version.h
 
 if HAVE_ALSA
diff --git a/desmume/src/common.cpp b/desmume/src/common.cpp
index 400536e43..fedd23a22 100644
--- a/desmume/src/common.cpp
+++ b/desmume/src/common.cpp
@@ -119,4 +119,4 @@ u32 strlen_ws(char *buf)		// length without last spaces
 		if (buf[i]!=32) return (i-1);		// space
 	}
 	return 0;
-}
\ No newline at end of file
+}
diff --git a/desmume/src/windows/Makefile.am b/desmume/src/windows/Makefile.am
deleted file mode 100644
index 5fcc52a37..000000000
--- a/desmume/src/windows/Makefile.am
+++ /dev/null
@@ -1,37 +0,0 @@
-include $(top_srcdir)/src/desmume.mk
-
-EXTRA_DIST = DeSmuME.ico \
-	 Makefile.win \
-	resources.rc
-bin_PROGRAMS = desmume
-desmume_SOURCES = \
-	afxres.h aviout.h config.h \
-        CWindow.cpp CWindow.h \
-        disView.cpp disView.h ginfo.cpp ginfo.h \
-        IORegView.cpp IORegView.h \
-        main.cpp main.h mapView.cpp mapView.h memView.cpp memView.h \
-        oamView.cpp oamView.h palView.cpp palView.h \
-        resource.h \
-        snddx.cpp snddx.h \
-        tileView.cpp tileView.h \
-	FirmConfig.cpp FirmConfig.h \
-	AboutBox.cpp AboutBox.h \
-	colorctrl.cpp colorctrl.h \
-	lightView.cpp lightView.h \
-	matrixView.cpp matrixView.h \
-	aviout.cpp console.cpp console.h \
-	inputdx.cpp inputdx.h ogl.cpp \
-	throttle.cpp throttle.h windriver.h \
-	cheatsWin.cpp cheatsWin.h gbaslot_config.cpp gbaslot_config.h \
-	mic.cpp hotkey.cpp hotkey.h \
-	ram_search.cpp ram_search.h ramwatch.cpp ramwatch.h \
-	replay.cpp replay.h soundView.cpp soundView.h \
-	DeSmuME_2005.vcproj DeSmuME_2008.vcproj \
-	DeSmuME_Intel.icproj DeSmuME_Intel.vcproj DeSmuME_Intel.sln \
-	DeSmuME_x64.manifest DeSmuME_x86.manifest
-desmume_LDADD = ../libdesmume.a yopyop_private.o
-if HAVE_GDB_STUB
-desmume_LDADD += ../gdbstub/libgdbstub.a
-endif
-yopyop_private.o: resources.rc resource.h
-	windres resources.rc -o resources.o
diff --git a/desmume/src/windows/Makefile.win b/desmume/src/windows/Makefile.win
deleted file mode 100644
index e9c7d8ce8..000000000
--- a/desmume/src/windows/Makefile.win
+++ /dev/null
@@ -1,93 +0,0 @@
-# Project: DeSmuME
-# Makefile created by Dev-C++ 4.9.9.2
-
-CPP  = g++.exe
-CC   = gcc.exe
-WINDRES = windres.exe
-RES  = obj/yopyop_private.res
-OBJ  = obj/main.o obj/mem_view.o obj/des_view.o obj/ginfo.o obj/IORegView.o obj/palView.o obj/CWindow.o obj/tileView.o obj/mapView.o obj/oamView.o obj/arm_instructions.o obj/armcpu.o obj/bios.o obj/cp15.o obj/debug.o obj/Disassembler.o obj/FIFO.o obj/GPU.o obj/MMU.o obj/NDSSystem.o obj/thumb_instructions.o $(RES)
-LINKOBJ  = obj/main.o obj/mem_view.o obj/des_view.o obj/ginfo.o obj/IORegView.o obj/palView.o obj/CWindow.o obj/tileView.o obj/mapView.o obj/oamView.o obj/arm_instructions.o obj/armcpu.o obj/bios.o obj/cp15.o obj/debug.o obj/Disassembler.o obj/FIFO.o obj/GPU.o obj/MMU.o obj/NDSSystem.o obj/thumb_instructions.o $(RES)
-LIBS =  -L"lib" -mwindows  -s -march=pentium4 -msse2 
-INCS =  -I"include" 
-CXXINCS =  -I"lib/gcc/mingw32/3.4.2/include"  -I"include/c++/3.4.2/backward"  -I"include/c++/3.4.2/mingw32"  -I"include/c++/3.4.2"  -I"include" 
-BIN  = DeSmuME.exe
-CXXFLAGS = $(CXXINCS)   -fexpensive-optimizations -O3 -march=pentium4 -msse2
-CFLAGS = $(INCS)   -fexpensive-optimizations -O3 -march=pentium4 -msse2
-RM = rm -f
-
-.PHONY: all all-before all-after clean clean-custom
-
-all: all-before DeSmuME.exe all-after
-
-
-clean: clean-custom
-	${RM} $(OBJ) $(BIN)
-
-$(BIN): $(OBJ)
-	$(CPP) $(LINKOBJ) -o "DeSmuME.exe" $(LIBS)
-
-obj/main.o: main.cpp
-	$(CPP) -c main.cpp -o obj/main.o $(CXXFLAGS)
-
-obj/mem_view.o: mem_view.cpp
-	$(CPP) -c mem_view.cpp -o obj/mem_view.o $(CXXFLAGS)
-
-obj/des_view.o: des_view.cpp
-	$(CPP) -c des_view.cpp -o obj/des_view.o $(CXXFLAGS)
-
-obj/ginfo.o: ginfo.cpp
-	$(CPP) -c ginfo.cpp -o obj/ginfo.o $(CXXFLAGS)
-
-obj/IORegView.o: IORegView.cpp
-	$(CPP) -c IORegView.cpp -o obj/IORegView.o $(CXXFLAGS)
-
-obj/palView.o: palView.cpp
-	$(CPP) -c palView.cpp -o obj/palView.o $(CXXFLAGS)
-
-obj/CWindow.o: CWindow.cpp
-	$(CPP) -c CWindow.cpp -o obj/CWindow.o $(CXXFLAGS)
-
-obj/tileView.o: tileView.cpp
-	$(CPP) -c tileView.cpp -o obj/tileView.o $(CXXFLAGS)
-
-obj/mapView.o: mapView.cpp
-	$(CPP) -c mapView.cpp -o obj/mapView.o $(CXXFLAGS)
-
-obj/oamView.o: oamView.cpp
-	$(CPP) -c oamView.cpp -o obj/oamView.o $(CXXFLAGS)
-
-obj/arm_instructions.o: ../arm_instructions.cpp
-	$(CPP) -c ../arm_instructions.cpp -o obj/arm_instructions.o $(CXXFLAGS)
-
-obj/armcpu.o: ../armcpu.cpp
-	$(CPP) -c ../armcpu.cpp -o obj/armcpu.o $(CXXFLAGS)
-
-obj/bios.o: ../bios.cpp
-	$(CPP) -c ../bios.cpp -o obj/bios.o $(CXXFLAGS)
-
-obj/cp15.o: ../cp15.cpp
-	$(CPP) -c ../cp15.cpp -o obj/cp15.o $(CXXFLAGS)
-
-obj/debug.o: ../debug.c
-	$(CPP) -c ../debug.c -o obj/debug.o $(CXXFLAGS)
-
-obj/Disassembler.o: ../Disassembler.cpp
-	$(CPP) -c ../Disassembler.cpp -o obj/Disassembler.o $(CXXFLAGS)
-
-obj/FIFO.o: ../FIFO.cpp
-	$(CPP) -c ../FIFO.cpp -o obj/FIFO.o $(CXXFLAGS)
-
-obj/GPU.o: ../GPU.cpp
-	$(CPP) -c ../GPU.cpp -o obj/GPU.o $(CXXFLAGS)
-
-obj/MMU.o: ../MMU.cpp
-	$(CPP) -c ../MMU.cpp -o obj/MMU.o $(CXXFLAGS)
-
-obj/NDSSystem.o: ../NDSSystem.cpp
-	$(CPP) -c ../NDSSystem.cpp -o obj/NDSSystem.o $(CXXFLAGS)
-
-obj/thumb_instructions.o: ../thumb_instructions.cpp
-	$(CPP) -c ../thumb_instructions.cpp -o obj/thumb_instructions.o $(CXXFLAGS)
-
-obj/yopyop_private.res: yopyop_private.rc resources.rc yopyop_private.rc 
-	$(WINDRES) -i yopyop_private.rc --input-format=rc -o obj/yopyop_private.res -O coff