diff --git a/Makefile.am b/Makefile.am
index 2d58027c5..c1a13fd7d 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -14,7 +14,6 @@ EXTRA_DIST = \
 	lua51/Makefile \
 	lua51/README \
 	lua51/README.Aegisub \
-	lua51/doc/ \
 	lua51/doc/contents.html \
 	lua51/doc/logo.gif \
 	lua51/doc/lua.css \
@@ -22,7 +21,6 @@ EXTRA_DIST = \
 	lua51/doc/readme.html \
 	lua51/lua51.vcproj \
 	lua51/lua51_vc8.vcproj \
-	lua51/src/ \
 	lua51/src/Makefile \
 	lua51/src/lapi.c \
 	lua51/src/lapi.h \
diff --git a/auto3/Makefile.am b/auto3/Makefile.am
index 87c623d2e..438299038 100644
--- a/auto3/Makefile.am
+++ b/auto3/Makefile.am
@@ -36,7 +36,6 @@ libaegisub_auto3_la_SOURCES = \
 EXTRA_DIST = \
 	auto3.sln \
 	auto3.vcproj \
-	lua/ \
 	lua/COPYRIGHT \
 	lua/README
 	lua/README.Aegisub \
@@ -44,13 +43,33 @@ EXTRA_DIST = \
 	lua/DIFFS \
 	lua/HISTORY \
 	lua/lua.vcproj \
-	lua/doc/ \
 	lua/doc/contents.html \
 	lua/doc/manual.html \
 	lua/doc/readme.html \
-	lua/doc/logo.gif \
-	lua/include/ \
+	lua/doc/logo.gif
+
+noinst_HEADERS = \
+	auto3.h \
 	lua/include/lua.h \
 	lua/include/lualib.h \
-	lua/include/lauxlib.h
+	lua/include/lauxlib.h \
+	lua/src/lapi.h \
+	lua/src/lcode.h \
+	lua/src/ldebug.h \
+	lua/src/ldo.h \
+	lua/src/lfunc.h \
+	lua/src/lgc.h \
+	lua/src/llex.h \
+	lua/src/llimits.h \
+	lua/src/lmem.h \
+	lua/src/lobject.h \
+	lua/src/lopcodes.h \
+	lua/src/lparser.h \
+	lua/src/lstate.h \
+	lua/src/lstring.h \
+	lua/src/ltable.h \
+	lua/src/ltm.h \
+	lua/src/lundump.h \
+	lua/src/lzio.h \
+	lua/src/lvm.h
 
diff --git a/autogen.sh b/autogen.sh
index 6ade894da..646744170 100644
--- a/autogen.sh
+++ b/autogen.sh
@@ -7,7 +7,7 @@ cat > automation/Makefile.am <<EOF
 ## Please edit autogen.sh if you need to modify this file.
 
 automationdir = \$(datarootdir)/aegisub/automation
-automation_DATA = \\
+dist_automation_DATA = \\
 EOF
 
 find automation/ -name '*.lua' -or -name '*.rb' -or -name '*.auto3' -or -name '*.txt' | sed '{s/^automation\//\t/; s/$/ \\/}' >> automation/Makefile.am