Index: benchmark/Makefile.am
===================================================================
--- benchmark/Makefile.am	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ benchmark/Makefile.am	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -14,4 +14,6 @@
 ## Update Count     : 25
 ###############################################################################
+
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 
 # applies to both programs
Index: benchmark/Makefile.in
===================================================================
--- benchmark/Makefile.in	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ benchmark/Makefile.in	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -253,4 +253,5 @@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 CFACOMPILE = $(CFACC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CFAFLAGS) $(CFAFLAGS) $(AM_CFLAGS) $(CFLAGS)
 AM_V_CFA = $(am__v_CFA_@AM_V@)
Index: configure
===================================================================
--- configure	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ configure	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -3289,6 +3289,9 @@
 # Create variables for commonly used targets
 
-TOP_SRCDIR=$ac_pwd/$ac_confdir/
-TOP_BUILDDIR=$ac_pwd/
+TOP_SRCDIR=$(readlink -f $ac_confdir/)
+TOP_BUILDDIR=$(readlink -f $ac_pwd/)
+
+echo ${TOP_SRCDIR}
+echo ${TOP_BUILDDIR}
 
 
Index: configure.ac
===================================================================
--- configure.ac	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ configure.ac	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -80,6 +80,9 @@
 # Create variables for commonly used targets
 
-TOP_SRCDIR=$ac_pwd/$ac_confdir/
-TOP_BUILDDIR=$ac_pwd/
+TOP_SRCDIR=$(readlink -f $ac_confdir/)
+TOP_BUILDDIR=$(readlink -f $ac_pwd/)
+
+echo ${TOP_SRCDIR}
+echo ${TOP_BUILDDIR}
 
 AC_DEFINE_UNQUOTED(TOP_SRCDIR, "$TOP_SRCDIR", [Top src directory])
Index: driver/Makefile.am
===================================================================
--- driver/Makefile.am	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ driver/Makefile.am	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -14,4 +14,6 @@
 ## Update Count     : 14
 ###############################################################################
+
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 
 # applies to both programs
Index: driver/Makefile.in
===================================================================
--- driver/Makefile.in	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ driver/Makefile.in	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -298,4 +298,5 @@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 
 # applies to both programs
Index: libcfa/prelude/Makefile.am
===================================================================
--- libcfa/prelude/Makefile.am	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ libcfa/prelude/Makefile.am	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -16,5 +16,5 @@
 
 # create object files in directory with source files
-AUTOMAKE_OPTIONS = subdir-objects
+AUTOMAKE_OPTIONS = foreign subdir-objects
 
 # put into lib for now
Index: src/Makefile.am
===================================================================
--- src/Makefile.am	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ src/Makefile.am	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -16,5 +16,5 @@
 
 # create object files in directory with source files
-AUTOMAKE_OPTIONS = subdir-objects
+AUTOMAKE_OPTIONS = foreign subdir-objects
 
 SRC = main.cc \
Index: src/Makefile.in
===================================================================
--- src/Makefile.in	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ src/Makefile.in	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -445,5 +445,5 @@
 
 # create object files in directory with source files
-AUTOMAKE_OPTIONS = subdir-objects
+AUTOMAKE_OPTIONS = foreign subdir-objects
 SRC = main.cc MakeLibCfa.cc CompilationState.cc CodeGen/Generate.cc \
 	CodeGen/CodeGenerator.cc CodeGen/GenType.cc \
Index: tests/Makefile.am
===================================================================
--- tests/Makefile.am	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ tests/Makefile.am	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -15,4 +15,5 @@
 ###############################################################################
 
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 
 debug=yes
Index: tests/Makefile.in
===================================================================
--- tests/Makefile.in	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ tests/Makefile.in	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -295,4 +295,5 @@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 debug = yes
 installed = no
Index: tests/preempt_longrun/Makefile.am
===================================================================
--- tests/preempt_longrun/Makefile.am	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ tests/preempt_longrun/Makefile.am	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -14,4 +14,6 @@
 ## Update Count     : 0
 ###############################################################################
+
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 
 repeats=10
Index: tests/preempt_longrun/Makefile.in
===================================================================
--- tests/preempt_longrun/Makefile.in	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ tests/preempt_longrun/Makefile.in	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -454,4 +454,5 @@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 repeats = 10
 max_time = 600
Index: tools/Makefile.am
===================================================================
--- tools/Makefile.am	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ tools/Makefile.am	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -15,6 +15,8 @@
 ###############################################################################
 
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
+
 CC = @BACKEND_CC@
-CFLAGS = -Wall -Wextra -O2 -g
+AM_CFLAGS = -Wall -Wextra -O2 -g
 
 noinst_PROGRAMS = busy catchsig repeat watchdog
Index: tools/Makefile.in
===================================================================
--- tools/Makefile.in	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ tools/Makefile.in	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -202,5 +202,5 @@
 CFA_NAME = @CFA_NAME@
 CFA_PREFIX = @CFA_PREFIX@
-CFLAGS = -Wall -Wextra -O2 -g
+CFLAGS = @CFLAGS@
 CPP = @CPP@
 CPPFLAGS = @CPPFLAGS@
@@ -303,4 +303,6 @@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
+AM_CFLAGS = -Wall -Wextra -O2 -g
 busy_SOURCES = busy.c
 busy_LDFLAGS = -pthread
Index: tools/prettyprinter/Makefile.am
===================================================================
--- tools/prettyprinter/Makefile.am	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ tools/prettyprinter/Makefile.am	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -1,11 +1,11 @@
 ######################## -*- Mode: Makefile-Automake -*- ######################
-## 
+##
 ## Cforall Version 1.0.0 Copyright (C) 2015 University of Waterloo
 ##
 ## The contents of this file are covered under the licence agreement in the
 ## file "LICENCE" distributed with Cforall.
-## 
-## Makefile.am -- 
-## 
+##
+## Makefile.am --
+##
 ## Author           : Peter A. Buhr
 ## Created On       : Wed Jun 28 12:07:10 2017
@@ -14,4 +14,6 @@
 ## Update Count     : 20
 ###############################################################################
+
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 
 BUILT_SOURCES = parser.hh
Index: tools/prettyprinter/Makefile.in
===================================================================
--- tools/prettyprinter/Makefile.in	(revision ea5b7d6404672e44c86d9619138a0e04d3c4b2dc)
+++ tools/prettyprinter/Makefile.in	(revision 0c1b5660b6f5a0957c905780ecc5883a812e52a7)
@@ -327,4 +327,5 @@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+AUTOMAKE_OPTIONS = foreign    # do not require all the GNU file names
 BUILT_SOURCES = parser.hh
 AM_YFLAGS = -d -t -v