diff --git a/.gitignore b/.gitignore
index d678d1598a..be10b24086 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,7 +31,6 @@
 /src/scp/Stellar-SCP.h
 /src/StellarCoreVersion.h
 /src/xdr/*.h
-/README
 /Makefile
 /Makefile.in
 /aclocal.m4
diff --git a/Makefile.am b/Makefile.am
index 9608b69ce8..588ded6313 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -7,7 +7,7 @@ ACLOCAL_AMFLAGS = -I m4
 include $(top_srcdir)/common.mk
 
 # Can't use SUBDIRS for sub-packages as we don't want make install going there
-DIST_SUBDIRS = $(SUBDIRS) $(PKGCONFIG_SUBDIRS)
+DIST_SUBDIRS = src $(PKGCONFIG_SUBDIRS)
 .PHONY: $(PKGCONFIG_SUBDIRS)
 $(PKGCONFIG_SUBDIRS):
 	cd $@ && $(MAKE) $(AM_MAKEFLAGS)
@@ -58,12 +58,6 @@ VALGRIND_FLAGS = --num-callers=30 --trace-children=yes \
 VALGRIND_SUPPRESSIONS_FILES = stellar-core.supp
 
 maintainer-clean-local:
-	+@echo rm -rf `sed -ne 's!^/!!p' .gitignore` Makefile.in
-	rm -rf `sed -ne 's!^/!!p' .gitignore` Makefile.in
-if USE_AFL_FUZZ
-	+@echo rm -rf fuzz-testcases fuzz-findings
-	rm -rf fuzz-testcases fuzz-findings
-endif
+	cd $(srcdir) && rm -rf `sed -ne 's!^/!!p' .gitignore` *~ .gitignore~
 
-README: README.md
-	$(AM_V_GEN)cp $< $@
+CLEANFILES = stellar*.log test-suite.log .gitignore~ *~
diff --git a/README b/README
new file mode 100644
index 0000000000..0f217dbebd
--- /dev/null
+++ b/README
@@ -0,0 +1 @@
+Please see README.md.
diff --git a/autogen.sh b/autogen.sh
index 03beb513ce..f268076ead 100755
--- a/autogen.sh
+++ b/autogen.sh
@@ -2,6 +2,12 @@
 
 # Public domain
 
+case "$0" in
+    */*)
+	cd $(dirname $0)
+	;;
+esac
+
 case "$1" in
     --skip-submodules|-s)
 	skip_submodules=yes
diff --git a/common.mk b/common.mk
index 87650b453b..82e6c7d5f3 100644
--- a/common.mk
+++ b/common.mk
@@ -1,10 +1,10 @@
 # Hand-written file with variables common to all makefiles
 
-CPPFLAGS = -DASIO_SEPARATE_COMPILATION=1 -DSQLITE_OMIT_LOAD_EXTENSION=1
-CPPFLAGS += -I"$(top_srcdir)" -I"$(top_srcdir)/src" -I"$(top_builddir)/src"
-CPPFLAGS += $(libsodium_CFLAGS) $(xdrpp_CFLAGS) $(libmedida_CFLAGS)	\
+AM_CPPFLAGS = -DASIO_SEPARATE_COMPILATION=1 -DSQLITE_OMIT_LOAD_EXTENSION=1
+AM_CPPFLAGS += -I"$(top_srcdir)" -I"$(top_srcdir)/src" -I"$(top_builddir)/src"
+AM_CPPFLAGS += $(libsodium_CFLAGS) $(xdrpp_CFLAGS) $(libmedida_CFLAGS)	\
 	$(soci_CFLAGS)
-CPPFLAGS += -I"$(top_srcdir)/lib"			\
+AM_CPPFLAGS += -I"$(top_srcdir)/lib"			\
 	-I"$(top_srcdir)/lib/autocheck/include"		\
 	-I"$(top_srcdir)/lib/cereal/include"		\
 	-I"$(top_srcdir)/lib/asio/include"		\
@@ -13,5 +13,5 @@ CPPFLAGS += -I"$(top_srcdir)/lib"			\
 	-I"$(top_srcdir)/lib/soci/src/backends/sqlite3"
 
 if USE_POSTGRES
-CPPFLAGS += -DUSE_POSTGRES=1 $(libpq_CFLAGS)
+AM_CPPFLAGS += -DUSE_POSTGRES=1 $(libpq_CFLAGS)
 endif # USE_POSTGRES
diff --git a/src/Makefile.am b/src/Makefile.am
index 07a94dbdef..0cf65d3741 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -54,4 +54,7 @@ fuzz-clean: always
 distclean-local: fuzz-clean
 endif # USE_AFL_FUZZ
 
+CLEANFILES = $(BUILT_SOURCES) *~ */*~
+MAINTAINERCLEANFILES = $(srcdir)/Makefile.in $(srcdir)/*~ $(srcdir)/*/*~
+
 EXTRA_DIST = $(SRC_X_FILES) src.mk