diff --git a/Makefile.am b/Makefile.am
index 75d502f1..f52ac92f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -7,33 +7,26 @@ CLEANFILES = default-config.h default-theme.h
 @MAINTAINER_MODE_TRUE@.PHONY: irssi-version.h
 
 default-config.h: $(srcdir)/irssi.conf
-	$(srcdir)/file2header.sh $(srcdir)/irssi.conf default_config > default-config.h
+	$(srcdir)/utils/file2header.sh $(srcdir)/irssi.conf default_config > default-config.h
 
-default-theme.h: $(srcdir)/default.theme
-	$(srcdir)/file2header.sh $(srcdir)/default.theme default_theme > default-theme.h
+default-theme.h: $(srcdir)/themes/default.theme
+	$(srcdir)/utils/file2header.sh $(srcdir)/themes/default.theme default_theme > default-theme.h
 
 irssi-version.h:
-	VERSION="$(VERSION)" $(srcdir)/irssi-version.sh $(srcdir) | \
-		cmp -s - $@ || VERSION="$(VERSION)" $(srcdir)/irssi-version.sh $(srcdir) >$@
+	VERSION="$(VERSION)" $(srcdir)/utils/irssi-version.sh $(srcdir) | \
+		cmp -s - $@ || VERSION="$(VERSION)" $(srcdir)/utils/irssi-version.sh $(srcdir) >$@
 
-SUBDIRS = src docs scripts
+SUBDIRS = src docs scripts themes utils
 
 confdir = $(sysconfdir)
 conf_DATA = irssi.conf
 
-themedir = $(datadir)/irssi/themes
-theme_DATA = default.theme colorless.theme
-
 pkginclude_HEADERS = irssi-config.h irssi-version.h
 
 EXTRA_DIST = \
 	ChangeLog \
 	autogen.sh \
 	README.md \
-	file2header.sh \
 	$(conf_DATA) \
-	$(theme_DATA) \
 	irssi-config.in \
-	irssi-icon.png \
-	irssi-version.sh \
-	syntax.pl
+	irssi-icon.png
diff --git a/autogen.sh b/autogen.sh
index a9e354c9..9feb0872 100755
--- a/autogen.sh
+++ b/autogen.sh
@@ -3,21 +3,24 @@
 
 PKG_NAME="Irssi"
 
-srcdir=`dirname $0`
+srcdir=`dirname "$0"`
 test -z "$srcdir" && srcdir=.
+mydir=`pwd`
 
-if test ! -f $srcdir/configure.ac; then
-    echo -n "**Error**: Directory \`$srcdir\' does not look like the"
+if test ! -f "$srcdir"/configure.ac; then
+    echo -n "**Error**: Directory \`$srcdir' does not look like the"
     echo " top-level $PKG_NAME directory"
     exit 1
 fi
 
+cd "$srcdir"
+
 # create help files
 echo "Creating help files..."
-perl syntax.pl
+perl utils/syntax.pl
 
 echo "Creating ChangeLog..."
-git log > $srcdir/ChangeLog
+git log > ChangeLog
 if test "$?" -ne 0; then
     echo "**Error**: ${PKG_NAME} Autogen must be run in a git clone, cannot proceed."
     exit 1
@@ -38,17 +41,19 @@ fi
 
 rm -f aclocal.m4
 echo "Running autoreconf ..."
-autoreconf -i || exit 1
+autoreconf -i || exit $?
+
+# make sure perl hashes have correct length
+find src/perl -name '*.c' -o -name '*.xs' -exec grep -n hv_store {} + | perl -l -ne 'if (/"(\w+)",\s*(\d+)/ && $2 != length $1) { $X=1; print "Incorrect key length in $_" } END { exit $X }'
+
+cd "$mydir"
 
 conf_flags="--enable-maintainer-mode"
 
 if test x$NOCONFIGURE = x; then
-  echo Running $srcdir/configure $conf_flags "$@" ...
-  $srcdir/configure $conf_flags "$@" \
+  echo Running "$srcdir"/configure $conf_flags "$@" ...
+  "$srcdir"/configure $conf_flags "$@" \
   && echo Now type \`make\' to compile $PKG_NAME || exit 1
 else
   echo Skipping configure process.
 fi
-
-# make sure perl hashes have correct length
-find src/perl -name '*.c' -o -name '*.xs' -exec grep -n hv_store {} + | perl -l -ne 'if (/"(\w+)",\s*(\d+)/ && $2 != length $1) { $X=1; print "Incorrect key length in $_" } END { exit $X }'
diff --git a/configure.ac b/configure.ac
index 9c026c5d..4b65d434 100644
--- a/configure.ac
+++ b/configure.ac
@@ -661,6 +661,8 @@ scripts/examples/Makefile
 docs/Makefile
 docs/help/Makefile
 docs/help/in/Makefile
+utils/Makefile
+themes/Makefile
 irssi-config
 ])
 
diff --git a/themes/Makefile.am b/themes/Makefile.am
new file mode 100644
index 00000000..ad0707c2
--- /dev/null
+++ b/themes/Makefile.am
@@ -0,0 +1,5 @@
+themedir = $(datadir)/irssi/themes
+theme_DATA = default.theme colorless.theme
+
+EXTRA_DIST = \
+	$(theme_DATA)
diff --git a/colorless.theme b/themes/colorless.theme
similarity index 100%
rename from colorless.theme
rename to themes/colorless.theme
diff --git a/default.theme b/themes/default.theme
similarity index 100%
rename from default.theme
rename to themes/default.theme
diff --git a/utils/Makefile.am b/utils/Makefile.am
new file mode 100644
index 00000000..be24c17f
--- /dev/null
+++ b/utils/Makefile.am
@@ -0,0 +1,4 @@
+EXTRA_DIST = \
+	file2header.sh \
+	irssi-version.sh \
+	syntax.pl
diff --git a/file2header.sh b/utils/file2header.sh
similarity index 100%
rename from file2header.sh
rename to utils/file2header.sh
diff --git a/irssi-version.sh b/utils/irssi-version.sh
similarity index 100%
rename from irssi-version.sh
rename to utils/irssi-version.sh
diff --git a/syncdocs.sh b/utils/syncdocs.sh
similarity index 98%
rename from syncdocs.sh
rename to utils/syncdocs.sh
index 1187eec9..e723edd2 100755
--- a/syncdocs.sh
+++ b/utils/syncdocs.sh
@@ -16,6 +16,7 @@ s{(<.*?)\sclass="(?:highlighter-rouge|highlight)"(.*?>)}{\1\2}g;'
 
 srcdir=`dirname "$0"`
 test -z "$srcdir" && srcdir=.
+srcdir="$srcdir"/..
 
 if test ! -f "$srcdir"/configure.ac; then
     echo -n "**Error**: Directory \`$srcdir' does not look like the"
@@ -94,7 +95,7 @@ cat "$srcdir"/docs/faq.html \
 	if ($_ eq "\n" && $state eq "Q") { $_ = ""; }
 	elsif (/^([QA]):/) { $state = $1 }
 	elsif ($_ ne "\n") { $_ = "   $_"; };
-' > docs/faq.txt
+' > "$srcdir"/docs/faq.txt
 
 cat "$srcdir"/docs/startup-HOWTO.html \
     | perl -pe "s/\\bhref=([\"\'])#.*?\\1//" \
diff --git a/syncscripts.sh b/utils/syncscripts.sh
similarity index 97%
rename from syncscripts.sh
rename to utils/syncscripts.sh
index eee95a5e..533b77cc 100755
--- a/syncscripts.sh
+++ b/utils/syncscripts.sh
@@ -7,6 +7,7 @@ scriptbase=https://scripts.irssi.org/scripts
 
 srcdir=`dirname "$0"`
 test -z "$srcdir" && srcdir=.
+srcdir="$srcdir"/..
 
 if test ! -f "$srcdir"/configure.ac; then
     echo -n "**Error**: Directory \`$srcdir' does not look like the"
diff --git a/syntax.pl b/utils/syntax.pl
similarity index 100%
rename from syntax.pl
rename to utils/syntax.pl