diff --git a/Makefile.in b/Makefile.in
index a2ac0b7..5cd19be 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -31,7 +31,7 @@ DOCDIR=@DOCDIR@
 CC = @CC@
 CCWARNFLAGS = @CCWARNFLAGS@
 OPTFLAGS = @CFLAGS@
-CPPFLAGS = @CPPFLAGS@ @SYSDEFS@ @EXTRA_DEFS@
+CPPFLAGS = @CPPFLAGS@
 
 DESTDIR=
 
@@ -75,9 +75,6 @@ chronyd : $(OBJS) $(EXTRA_OBJS)
 chronyc : $(CLI_OBJS)
 	$(CC) $(OPTFLAGS) -o chronyc $(CLI_OBJS) $(LDFLAGS) @READLINE_LINK@ $(LIBS) $(EXTRA_CLI_LIBS)
 
-conf.o : conf.c
-	$(CC) $(CFLAGS) $(CPPFLAGS) -DDEFAULT_CONF_DIR=\"$(SYSCONFDIR)\" -c $<
-
 client.o : client.c
 	$(CC) $(CFLAGS) $(CPPFLAGS) @READLINE_COMPILE@ -c $<
 
diff --git a/acquire.c b/acquire.c
index 0a02ee0..ff554ca 100644
--- a/acquire.c
+++ b/acquire.c
@@ -37,6 +37,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "acquire.h"
diff --git a/addrfilt.c b/addrfilt.c
index f280f0b..b6ae1ae 100644
--- a/addrfilt.c
+++ b/addrfilt.c
@@ -28,6 +28,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "addrfilt.h"
diff --git a/broadcast.c b/broadcast.c
index 11c8d70..1e3314b 100644
--- a/broadcast.c
+++ b/broadcast.c
@@ -24,6 +24,8 @@
   Deal with broadcast server functions.
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 #include "memory.h"
 
diff --git a/client.c b/client.c
index aad6944..d73e3dc 100644
--- a/client.c
+++ b/client.c
@@ -26,6 +26,8 @@
   from it whilst running.
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "candm.h"
diff --git a/clientlog.c b/clientlog.c
index 0243753..7666ffd 100644
--- a/clientlog.c
+++ b/clientlog.c
@@ -31,6 +31,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 #include "clientlog.h"
 #include "conf.h"
diff --git a/cmdmon.c b/cmdmon.c
index 04dd7d0..e0ea228 100644
--- a/cmdmon.c
+++ b/cmdmon.c
@@ -25,6 +25,8 @@
   Command and monitoring module in the main program
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "cmdmon.h"
diff --git a/cmdparse.c b/cmdparse.c
index f91a3da..0bf2492 100644
--- a/cmdparse.c
+++ b/cmdparse.c
@@ -26,6 +26,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "cmdparse.h"
diff --git a/conf.c b/conf.c
index 187f1e3..87050eb 100644
--- a/conf.c
+++ b/conf.c
@@ -36,6 +36,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "conf.h"
diff --git a/configure b/configure
index f3a9373..b0265c3 100755
--- a/configure
+++ b/configure
@@ -8,6 +8,8 @@
 #
 # =======================================================================
 
+rm -f config.h
+
 # This configure script determines the operating system type and version
 
 if [ "x${CC}" = "x" ]; then
@@ -69,7 +71,7 @@ test_code () {
 #}}}
 #{{{ usage
 usage () {
-  cat <<EOF;
+  cat <<EOF
 \`configure' configures tdl to adapt to many kinds of systems.
 
 Usage: ./configure [OPTION]...
@@ -133,6 +135,15 @@ EOF
 
 }
 #}}}
+#{{{
+add_def () {
+  if [ "x$2" = "x" ]; then
+    echo "#define $1 1" >> config.h
+  else
+    echo "#define $1 $2" >> config.h
+  fi
+}
+#}}}
 
 # ======================================================================
 
@@ -169,7 +180,7 @@ for option
 do
     case "$option" in
     --trace )
-      EXTRA_DEFS="-DTRACEON"
+      add_def TRACEON
     ;;
     --disable-readline )
       feat_readline=0
@@ -257,17 +268,17 @@ case $SYSTEM in
         4.* )
             EXTRA_OBJECTS="sys_sunos.o strerror.o"
             EXTRA_LIBS="-lkvm"
-            SYSDEFS="-DSUNOS"
+            add_def SUNOS
             echo "Configuring for SunOS (" $SYSTEM "version" $VERSION ")"
         ;;
         5.* )
             EXTRA_OBJECTS="sys_solaris.o"
             EXTRA_LIBS="-lsocket -lnsl -lkvm -lelf"
             EXTRA_CLI_LIBS="-lsocket -lnsl"
-            SYSDEFS="-DSOLARIS"
+            add_def SOLARIS
             echo "Configuring for Solaris (" $SYSTEM "SunOS version" $VERSION ")"
             if [ $VERSION = "5.3" ]; then
-                SYSDEFS="$SYSDEFS -DHAS_NO_BZERO"
+                add_def HAS_NO_BZERO
                 echo "Using memset() instead of bzero()"
             fi
         ;;
@@ -279,12 +290,12 @@ case $SYSTEM in
         try_rtc=1
         try_setsched=1
         try_lockmem=1
-        SYSDEFS="-DLINUX"
+        add_def LINUX
         echo "Configuring for " $SYSTEM
         if [ "${MACHINE}" = "alpha" ]; then
            echo "Enabling -mieee"
            # FIXME: Should really test for GCC
-           SYSDEFS="$SYSDEFS -mieee -DALPHA"
+           MYCFLAGS="$MYCFLAGS -mieee"
         fi
     ;;
 
@@ -293,7 +304,7 @@ case $SYSTEM in
         # be supported with the SunOS 4.x driver files.
         EXTRA_OBJECTS="sys_sunos.o strerror.o"
         EXTRA_LIBS="-lkvm"
-        SYSDEFS="-DSUNOS"
+        add_def SUNOS
         echo "Configuring for $SYSTEM (using SunOS driver)"
     ;;
     NetBSD-* )
@@ -308,13 +319,13 @@ case $SYSTEM in
         EXTRA_OBJECTS="sys_solaris.o"                
         EXTRA_LIBS="-lsocket -lnsl -lkvm -lelf"      
         EXTRA_CLI_LIBS="-lsocket -lnsl"                              
-        SYSDEFS="-DSOLARIS"                               
+        add_def SOLARIS
         echo "Configuring for Solaris (" $SYSTEM "SunOS version" $VERSION ")" 
     ;;                                                                        
     CYGWIN32_NT-i[3456]86 )
         EXTRA_OBJECTS="sys_winnt.o"
         EXTRA_LIBS=""
-        SYSDEFS="-DWINNT"
+        add_def WINNT
         echo "Configuring for Windows NT (Cygwin32)"
     ;;
     * )
@@ -336,11 +347,11 @@ else
 fi
   
 if test_code '<stdint.h>' 'stdint.h' '' '' ''; then
-  SYSDEFS="${SYSDEFS} -DHAS_STDINT_H"
+  add_def HAS_STDINT_H
 fi
 
 if test_code '<inttypes.h>' 'inttypes.h' '' '' ''; then
-  SYSDEFS="${SYSDEFS} -DHAS_INTTYPES_H"
+  add_def HAS_INTTYPES_H
 fi
 
 if [ $feat_ipv6 = "1" ] && \
@@ -350,7 +361,7 @@ if [ $feat_ipv6 = "1" ] && \
     n.sin6_addr = in6addr_any;
     return !inet_ntop(AF_INET6, &n.sin6_addr.s6_addr, p, sizeof(p));'
 then
-  SYSDEFS="${SYSDEFS} -DHAVE_IPV6"
+  add_def HAVE_IPV6
 fi
 
 if [ $feat_pps = "1" ] && \
@@ -360,7 +371,7 @@ if [ $feat_pps = "1" ] && \
     struct timespec ts;
     return time_pps_fetch(h, PPS_TSFMT_TSPEC, &i, &ts);'
 then
-  SYSDEFS="${SYSDEFS} -DHAVE_PPSAPI"
+  add_def HAVE_PPSAPI
 fi
 
 if [ $feat_linuxcaps = "1" ] && [ $try_linuxcaps = "1" ] && \
@@ -370,7 +381,7 @@ if [ $feat_linuxcaps = "1" ] && [ $try_linuxcaps = "1" ] && \
     '' '-lcap' \
     'prctl(PR_SET_KEEPCAPS, 1);cap_set_proc(cap_from_text("cap_sys_time=ep"));'
 then
-    EXTRA_DEFS="${EXTRA_DEFS} -DFEAT_LINUXCAPS=1"
+    add_def FEAT_LINUXCAPS
     EXTRA_LIBS="-lcap"
 fi
 
@@ -379,7 +390,7 @@ if [ $feat_rtc = "1" ] && [ $try_rtc = "1" ] && \
     'ioctl(1, RTC_UIE_ON&RTC_UIE_OFF&RTC_RD_TIME&RTC_SET_TIME, 0&RTC_UF);'
 then
     EXTRA_OBJECTS="$EXTRA_OBJECTS rtc_linux.o"
-    EXTRA_DEFS="$EXTRA_DEFS -DFEAT_RTC=1"
+    add_def FEAT_RTC
 fi
 
 if [ $try_setsched = "1" ] && \
@@ -390,7 +401,7 @@ if [ $try_setsched = "1" ] && \
      sched_get_priority_max(SCHED_FIFO);
      sched_setscheduler(0, SCHED_FIFO, &sched);'
 then
-  SYSDEFS="${SYSDEFS} -DHAVE_SCHED_SETSCHEDULER"
+  add_def HAVE_SCHED_SETSCHEDULER
 fi
 
 if [ $try_lockmem = "1" ] && \
@@ -401,12 +412,12 @@ if [ $try_lockmem = "1" ] && \
      setrlimit(RLIMIT_MEMLOCK, &rlim);
      mlockall(MCL_CURRENT|MCL_FUTURE);'
 then
-  SYSDEFS="${SYSDEFS} -DHAVE_MLOCKALL"
+  add_def HAVE_MLOCKALL
 fi
 
 if [ $feat_forcednsretry = "1" ]
 then
-    EXTRA_DEFS="$EXTRA_DEFS -DFORCE_DNSRETRY=1"
+  add_def FORCE_DNSRETRY
 fi
 
 READLINE_COMPILE=""
@@ -417,7 +428,9 @@ if [ $feat_readline = "1" ]; then
       "$readline_inc" "$readline_lib -ledit" \
       'add_history(readline("prompt"));'
     then
-      READLINE_COMPILE="-DFEAT_READLINE=1 -DUSE_EDITLINE=1 $readline_inc"
+      add_def FEAT_READLINE
+      add_def USE_EDITLINE
+      READLINE_COMPILE="$readline_inc"
       READLINE_LINK="$readline_lib -ledit"
     fi
   fi
@@ -427,7 +440,8 @@ if [ $feat_readline = "1" ]; then
       "$readline_inc" "$readline_lib $ncurses_lib -lreadline -lncurses" \
       'add_history(readline("prompt"));'
     then
-      READLINE_COMPILE="-DFEAT_READLINE=1 $readline_inc"
+      add_def FEAT_READLINE
+      READLINE_COMPILE="$readline_inc"
       READLINE_LINK="$readline_lib $ncurses_lib -lreadline -lncurses"
     fi
   fi
@@ -478,6 +492,8 @@ if [ "x$SETDOCDIR" != "x" ]; then
   DOCDIR=$SETDOCDIR
 fi
 
+add_def DEFAULT_CONF_DIR "\"$SYSCONFDIR\""
+
 sed -e "s%@EXTRA_OBJECTS@%${EXTRA_OBJECTS}%;\
 	s%@CC@%${MYCC}%;\
 	s%@CFLAGS@%${MYCFLAGS}%;\
@@ -486,8 +502,6 @@ sed -e "s%@EXTRA_OBJECTS@%${EXTRA_OBJECTS}%;\
 	s%@LIBS@%${LIBS}%;\
 	s%@LDFLAGS@%${MYLDFLAGS}%;\
 	s%@EXTRA_LIBS@%${EXTRA_LIBS}%;\
-	s%@SYSDEFS@%${SYSDEFS}%;\
-	s%@EXTRA_DEFS@%${EXTRA_DEFS}%;\
 	s%@EXTRA_CLI_LIBS@%${EXTRA_CLI_LIBS}%;\
 	s%@READLINE_COMPILE@%${READLINE_COMPILE}%;\
 	s%@READLINE_LINK@%${READLINE_LINK}%;\
diff --git a/keys.c b/keys.c
index eda42c9..68a1f1b 100644
--- a/keys.c
+++ b/keys.c
@@ -25,6 +25,8 @@
 
   */
 
+#include "config.h"
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
diff --git a/local.c b/local.c
index a48ff87..8017512 100644
--- a/local.c
+++ b/local.c
@@ -28,6 +28,8 @@
   They interface with the system specific driver files in sys_*.c
   */
 
+#include "config.h"
+
 #include <assert.h>
 #include <stddef.h>
 
diff --git a/logging.c b/logging.c
index ff8832f..282d86e 100644
--- a/logging.c
+++ b/logging.c
@@ -25,6 +25,8 @@
   Module to handle logging of diagnostic information
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "main.h"
diff --git a/main.c b/main.c
index 93148fc..f7db900 100644
--- a/main.c
+++ b/main.c
@@ -25,6 +25,8 @@
   The main program
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "main.h"
diff --git a/manual.c b/manual.c
index 16686de..93a9617 100644
--- a/manual.c
+++ b/manual.c
@@ -30,6 +30,8 @@
 
   */
 
+#include "config.h"
+
 #include <stddef.h>
 
 #include "manual.h"
diff --git a/md5.c b/md5.c
index f997a6e..e7a1121 100644
--- a/md5.c
+++ b/md5.c
@@ -37,6 +37,8 @@
  ***********************************************************************
  */
 
+#include "config.h"
+
 #include "md5.h"
 
 /*
diff --git a/mkdirpp.c b/mkdirpp.c
index 65bc9b2..88e29da 100644
--- a/mkdirpp.c
+++ b/mkdirpp.c
@@ -26,6 +26,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "mkdirpp.h"
diff --git a/nameserv.c b/nameserv.c
index 268ee2e..1770845 100644
--- a/nameserv.c
+++ b/nameserv.c
@@ -26,6 +26,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "nameserv.h"
diff --git a/ntp_core.c b/ntp_core.c
index 639b350..6c8a4ea 100644
--- a/ntp_core.c
+++ b/ntp_core.c
@@ -25,6 +25,8 @@
   Core NTP protocol engine
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "ntp_core.h"
diff --git a/ntp_io.c b/ntp_io.c
index baaf79a..9bad2bc 100644
--- a/ntp_io.c
+++ b/ntp_io.c
@@ -26,6 +26,8 @@
   This file deals with the IO aspects of reading and writing NTP packets
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "ntp_io.h"
diff --git a/ntp_sources.c b/ntp_sources.c
index d773978..43a5d91 100644
--- a/ntp_sources.c
+++ b/ntp_sources.c
@@ -27,6 +27,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "ntp_sources.h"
diff --git a/pktlength.c b/pktlength.c
index 74f35db..a2682f7 100644
--- a/pktlength.c
+++ b/pktlength.c
@@ -26,6 +26,8 @@
   integer endianness within the structures.
 
   */
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "util.h"
diff --git a/refclock.c b/refclock.c
index 6fd3527..edb743d 100644
--- a/refclock.c
+++ b/refclock.c
@@ -25,6 +25,8 @@
 
   */
 
+#include "config.h"
+
 #include "refclock.h"
 #include "reference.h"
 #include "conf.h"
diff --git a/refclock_pps.c b/refclock_pps.c
index 0a28b06..3a7ae1e 100644
--- a/refclock_pps.c
+++ b/refclock_pps.c
@@ -25,6 +25,8 @@
 
   */
 
+#include "config.h"
+
 #include "refclock.h"
 
 #if HAVE_PPSAPI
diff --git a/refclock_shm.c b/refclock_shm.c
index 083a06c..b9edea4 100644
--- a/refclock_shm.c
+++ b/refclock_shm.c
@@ -25,6 +25,8 @@
 
   */
 
+#include "config.h"
+
 #include "refclock.h"
 #include "logging.h"
 #include "util.h"
diff --git a/refclock_sock.c b/refclock_sock.c
index b4140dc..79e0e54 100644
--- a/refclock_sock.c
+++ b/refclock_sock.c
@@ -25,6 +25,8 @@
 
   */
 
+#include "config.h"
+
 #include "refclock.h"
 #include "logging.h"
 #include "util.h"
diff --git a/reference.c b/reference.c
index 14f6199..2c58b3b 100644
--- a/reference.c
+++ b/reference.c
@@ -25,6 +25,8 @@
   This module keeps track of the source which we are claiming to be
   our reference, for the purposes of generating outgoing NTP packets */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "memory.h"
diff --git a/regress.c b/regress.c
index 1613d55..9322d1f 100644
--- a/regress.c
+++ b/regress.c
@@ -26,6 +26,8 @@
 
   */
 
+#include "config.h"
+
 #include <assert.h>
 #include <math.h>
 
diff --git a/rtc.c b/rtc.c
index 612f5b0..4010900 100644
--- a/rtc.c
+++ b/rtc.c
@@ -23,6 +23,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "rtc.h"
diff --git a/rtc_linux.c b/rtc_linux.c
index 5fbcf0c..7f53da8 100644
--- a/rtc_linux.c
+++ b/rtc_linux.c
@@ -26,6 +26,8 @@
 
   */
 
+#include "config.h"
+
 #if defined LINUX
 
 #ifdef sparc
diff --git a/sched.c b/sched.c
index 3da75bd..c70e195 100644
--- a/sched.c
+++ b/sched.c
@@ -26,6 +26,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "sched.h"
diff --git a/sources.c b/sources.c
index bc515e9..5b022f3 100644
--- a/sources.c
+++ b/sources.c
@@ -28,6 +28,8 @@
 
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "sources.h"
diff --git a/sourcestats.c b/sourcestats.c
index bdb07dd..e36356a 100644
--- a/sourcestats.c
+++ b/sourcestats.c
@@ -26,6 +26,8 @@
   analysis on the samples obtained from the sources,
   to determined frequencies and error bounds. */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "sourcestats.h"
diff --git a/strerror.c b/strerror.c
index 7928dc5..8396142 100644
--- a/strerror.c
+++ b/strerror.c
@@ -24,6 +24,8 @@
   Replacement strerror function for systems that don't have it
   */
 
+#include "config.h"
+
 #ifdef SUNOS
 
 #include <errno.h>
diff --git a/sys.c b/sys.c
index ac73ec4..6c752fa 100644
--- a/sys.c
+++ b/sys.c
@@ -25,6 +25,8 @@
   in the various operating-system specific modules
   */
 
+#include "config.h"
+
 #include "sys.h"
 #include "logging.h"
 
diff --git a/sys_linux.c b/sys_linux.c
index 7370d22..441e6e4 100644
--- a/sys_linux.c
+++ b/sys_linux.c
@@ -27,6 +27,8 @@
 
   */
 
+#include "config.h"
+
 #ifdef LINUX
 
 #include <sys/time.h>
diff --git a/sys_netbsd.c b/sys_netbsd.c
index ada0e65..863f572 100644
--- a/sys_netbsd.c
+++ b/sys_netbsd.c
@@ -25,6 +25,8 @@
   Driver file for the NetBSD operating system.
   */
 
+#include "config.h"
+
 #ifdef __NetBSD__
 
 #include <kvm.h>
diff --git a/sys_solaris.c b/sys_solaris.c
index e08a602..db40091 100644
--- a/sys_solaris.c
+++ b/sys_solaris.c
@@ -24,6 +24,8 @@
   Driver file for Solaris operating system
   */
 
+#include "config.h"
+
 #ifdef SOLARIS
 
 #include <kvm.h>
diff --git a/sys_sunos.c b/sys_sunos.c
index da38e46..5178c5a 100644
--- a/sys_sunos.c
+++ b/sys_sunos.c
@@ -24,6 +24,8 @@
   Driver file for the SunOS 4.1.x operating system.
   */
 
+#include "config.h"
+
 #ifdef SUNOS
 
 #include <kvm.h>
diff --git a/tempcomp.c b/tempcomp.c
index c92d2c3..55bd091 100644
--- a/tempcomp.c
+++ b/tempcomp.c
@@ -25,6 +25,8 @@
 
   */
 
+#include "config.h"
+
 #include "conf.h"
 #include "local.h"
 #include "memory.h"
diff --git a/util.c b/util.c
index 2fe4763..0761c94 100644
--- a/util.c
+++ b/util.c
@@ -25,6 +25,8 @@
   Various utility functions
   */
 
+#include "config.h"
+
 #include "sysincl.h"
 
 #include "util.h"
diff --git a/wrap_adjtimex.c b/wrap_adjtimex.c
index 740e455..34e8251 100644
--- a/wrap_adjtimex.c
+++ b/wrap_adjtimex.c
@@ -29,6 +29,8 @@
 
   */
 
+#include "config.h"
+
 #ifdef LINUX
 
 #define _LOOSE_KERNEL_NAMES