diff --git a/aegisub/FFmpegSource2/Makefile.am b/aegisub/FFmpegSource2/Makefile.am
index 67d384ecb..f9cdfd92a 100644
--- a/aegisub/FFmpegSource2/Makefile.am
+++ b/aegisub/FFmpegSource2/Makefile.am
@@ -1,6 +1,6 @@
 noinst_LIBRARIES = libffmpegsource2_aegisub.a
 
-AM_CPPFLAGS = -I../aegisub -D__UNIX__ -DHAVE_STRLCPY @LIBAVFORMAT_CFLAGS@ @LIBAVCODEC_CFLAGS@ @LIBSWSCALE_CFLAGS@ @LIBAVUTIL_CFLAGS@ @LIBPOSTPROC_CFLAGS@
+AM_CPPFLAGS = -I../src -D__UNIX__ -DHAVE_STRLCPY @LIBAVFORMAT_CFLAGS@ @LIBAVCODEC_CFLAGS@ @LIBSWSCALE_CFLAGS@ @LIBAVUTIL_CFLAGS@ @LIBPOSTPROC_CFLAGS@
 
 
 libffmpegsource2_aegisub_a_SOURCES = \
diff --git a/aegisub/Makefile.am b/aegisub/Makefile.am
index edcb87dd3..41e2337db 100644
--- a/aegisub/Makefile.am
+++ b/aegisub/Makefile.am
@@ -22,7 +22,7 @@ SUBDIRS = \
 	$(auto3) \
     $(libass) \
 	$(ffmpegsource) \
-	aegisub \
+	src \
 	automation \
 	po \
 	desktop
diff --git a/aegisub/autogen.sh b/aegisub/autogen.sh
index 15eef989b..fab8833b8 100755
--- a/aegisub/autogen.sh
+++ b/aegisub/autogen.sh
@@ -34,7 +34,7 @@ test -z "$srcdir" && srcdir=.
 ORIGDIR=`pwd`
 cd $srcdir
 
-test -d aegisub || {
+test -d src || {
     echo
     echo "You must run this script in the top-level $PROJECT directory."
     echo
@@ -282,19 +282,19 @@ fi
 
 echo "--- Converting BMP resource files -> XPM ---"
 # BMP -> XPM via src/res.rc
-cat ${srcdir}/aegisub/res.rc | ${BIN_AWK} -f ${srcdir}/scripts/unix-gen-xpm.awk BIN_CONVERT="$BIN_CONVERT" > ${srcdir}/aegisub/bitmaps/Makefile.bitmaps
-cd ${srcdir}/aegisub/bitmaps
+cat ${srcdir}/src/res.rc | ${BIN_AWK} -f ${srcdir}/scripts/unix-gen-xpm.awk BIN_CONVERT="$BIN_CONVERT" > ${srcdir}/src/bitmaps/Makefile.bitmaps
+cd ${srcdir}/src/bitmaps
 make -f Makefile.bitmaps
 cd ${srcdir}
 
 $BIN_AWK '/BITMAP/ { image[count] = $1; ++count} END { printf("EXTRA_DIST="); for (v in image) printf(" \\\n	%s_xpm.xpm", image[v])}' \
-  ${srcdir}/aegisub/res.rc \
-  > ${srcdir}/aegisub/bitmaps/Makefile.am
+  ${srcdir}/src/res.rc \
+  > ${srcdir}/src/bitmaps/Makefile.am
 
 echo "--- Generating libresrc/resrc.cpp, libresrc/libresrc.h from res.rc ---"
-$BIN_AWK -f scripts/unix-gen-res.awk ${srcdir}/aegisub/res.rc \
-  RESRC_CPP="${srcdir}/aegisub/libresrc/resrc.cpp" \
-  RESRC_H="${srcdir}/aegisub/libresrc/libresrc.h"
+$BIN_AWK -f scripts/unix-gen-res.awk ${srcdir}/src/res.rc \
+  RESRC_CPP="${srcdir}/src/libresrc/resrc.cpp" \
+  RESRC_H="${srcdir}/src/libresrc/libresrc.h"
 
 rm -rf autom4te.cache
 
diff --git a/aegisub/configure.in b/aegisub/configure.in
index 8cf77d4d3..6696c2cb0 100644
--- a/aegisub/configure.in
+++ b/aegisub/configure.in
@@ -36,7 +36,7 @@ m4_define([wx_required_version], [2.8.1])
 # Setup
 #######
 AC_INIT([Aegisub], [aegisub_version],, [aegisub])
-AC_CONFIG_SRCDIR([aegisub/main.cpp])
+AC_CONFIG_SRCDIR([src/main.cpp])
 AM_INIT_AUTOMAKE
 AC_CONFIG_HEADER([acconf.h])
 AC_GNU_SOURCE
@@ -1257,10 +1257,10 @@ AC_DEFINE_UNQUOTED([DEFAULT_PLAYER_AUDIO], ["$default_player_audio"], [Default a
 # Makefiles
 AC_CONFIG_FILES([
 Makefile
-aegisub/Makefile
-aegisub/bitmaps/Makefile
-aegisub/libresrc/Makefile
-aegisub/libosxutil/Makefile
+src/Makefile
+src/bitmaps/Makefile
+src/libresrc/Makefile
+src/libosxutil/Makefile
 universalchardet/Makefile
 FFmpegSource2/Makefile
 auto3/Makefile
diff --git a/aegisub/libass/Makefile.am b/aegisub/libass/Makefile.am
index f410e52f9..ce5edb853 100644
--- a/aegisub/libass/Makefile.am
+++ b/aegisub/libass/Makefile.am
@@ -1,6 +1,6 @@
 noinst_LIBRARIES = libass_aegisub.a
 
-AM_CPPFLAGS = -I../aegisub @FREETYPE_CFLAGS@ -DCONFIG_ICONV -DCONFIG_FONTCONFIG @FONTCONFIG_CFLAGS@ @ICONV_CFLAGS@
+AM_CPPFLAGS = -I../src @FREETYPE_CFLAGS@ -DCONFIG_ICONV -DCONFIG_FONTCONFIG @FONTCONFIG_CFLAGS@ @ICONV_CFLAGS@
 
 if BUILD_DARWIN
 AM_CPPFLAGS += -DBUILD_DARWIN