diff --git a/afm/Makefile.in b/afm/Makefile.in
index 25b22af432c..60237a7480a 100644
--- a/afm/Makefile.in
+++ b/afm/Makefile.in
@@ -11,7 +11,15 @@ subdir = afm
 include $(top_builddir)/Makeconf
 
 distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir) && ls Makefile.in *.afm *.lt1)
+DISTFILES = Makefile.in \
+	agd_____.lt1 agdo____.lt1 agw_____.lt1 agwo____.lt1 bkd_____.lt1 \
+	bkdi____.lt1 bkl_____.lt1 bkli____.lt1 cob_____.lt1 cobo____.lt1 \
+	com_____.lt1 coo_____.lt1 hv______.lt1 hvb_____.lt1 hvbo____.lt1 \
+	hvn_____.lt1 hvnb____.lt1 hvnbo___.lt1 hvno____.lt1 hvo_____.lt1 \
+	ncb_____.lt1 ncbi____.lt1 nci_____.lt1 ncr_____.lt1 pob_____.lt1 \
+	pobi____.lt1 poi_____.lt1 por_____.lt1 tib_____.lt1 tibi____.lt1 \
+	tii_____.lt1 tir_____.lt1 \
+	sy______.afm
 
 all: Makefile R
 
diff --git a/src/appl/Makefile.in b/src/appl/Makefile.in
index a3ac7edc6ae..a8327068827 100644
--- a/src/appl/Makefile.in
+++ b/src/appl/Makefile.in
@@ -10,15 +10,11 @@ subdir = src/appl
 
 include $(top_builddir)/Makeconf
 
-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir); \
-	       ls COPYRIGHT COPYRIGHT.ftn Makefile.in ROUTINES *.[cfh])
-
 ## All functions/subroutines to be called via .C() or .Fortran() must
 ## also have an entry in `./ROUTINES' in order to be ``pre-dyn.loaded'';
 ## see `../unix/dynload.c'.
 
-SRCS_C = \
+SOURCES_C = \
 	S_compat.c \
 	approx.c \
 	bakslv.c \
@@ -42,49 +38,53 @@ SRCS_C = \
 	strsignif.c \
 	tabulate.c \
 	zeroin.c
-DEPS = $(SRCS_C:.c=.d)
-OBJS = $(SRCS_C:.c=.o) \
-	$(BLAS) \
-	ch2inv.o \
-	chol.o \
-	dpbfa.o \
-	dpbsl.o \
-	dpoco.o \
-	dpodi.o \
-	dpofa.o \
-	dposl.o \
-	dqrdc.o \
-	dqrdc2.o \
-        dqrls.o \
-	dqrsl.o \
-	dqrutl.o \
-	dsvdc.o \
-	dtrco.o \
-	dtrsl.o \
-	eigen.o \
-	fmin.o \
-	lminfl.o \
-	uncmin.o
+SOURCES_F = \
+	ch2inv.f \
+	chol.f \
+	dpbfa.f \
+	dpbsl.f \
+	dpoco.f \
+	dpodi.f \
+	dpofa.f \
+	dposl.f \
+	dqrdc.f \
+	dqrdc2.f \
+        dqrls.f \
+	dqrsl.f \
+	dqrutl.f \
+	dsvdc.f \
+	dtrco.f \
+	dtrsl.f \
+	eigen.f \
+	fmin.f \
+	lminfl.f \
+	uncmin.f
+DEPENDS = $(SOURCES_C:.c=.d)
+OBJECTS = $(SOURCES_C:.c=.o) $(SOURCES_F:.f=.o) $(BLAS)
+
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+DISTFILES = COPYRIGHT COPYRIGHT.ftn Makefile.in README ROUTINES \
+	$(SOURCES_C) $(SOURCES_F) blas.f
 
 LIB = libappl.a
 
 all: Makefile Makedeps R
 
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status $(DEPS)
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status $(DEPENDS)
 	@cd $(top_builddir) && \
 	  CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= \
 	  $(SHELL) ./config.status
 
 Makedeps: Makefile
-	@cat $(DEPS) >> Makefile
+	@cat $(DEPENDS) >> Makefile
 	@touch $@
 
 R: Makefile
 	@$(MAKE) Makedeps
 	@$(MAKE) $(LIB)
 
-$(LIB):	$(OBJS)
-	$(AR) cr $(LIB) $(OBJS)
+$(LIB):	$(OBJECTS)
+	$(AR) cr $(LIB) $(OBJECTS)
 	$(RANLIB) $(LIB)
 
 mostlyclean: clean
diff --git a/src/gnome/Makefile.in b/src/gnome/Makefile.in
index b8567970b04..c0e9752a175 100644
--- a/src/gnome/Makefile.in
+++ b/src/gnome/Makefile.in
@@ -12,10 +12,7 @@ include $(top_builddir)/Makeconf
 
 ALL_CPPFLAGS = $(GNOME_INCLUDEDIR) $(R_XTRA_CPPFLAGS) $(X_CFLAGS) $(CPPFLAGS) $(DEFS)
 
-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir) && ls Makefile.in *.[cfh])
-
-SRCS = \
+SOURCES = \
 	../unix/dataentry.c \
 	../unix/devPS.c \
 	../unix/devPicTeX.c \
@@ -33,8 +30,23 @@ SRCS = \
 	terminal-menu.c \
 	terminal-prefs.c \
 	terminal-toolbar.c
-DEPS = $(SRCS:.c=.d)
-OBJS = $(SRCS:.c=.o)
+DEPENDS = $(SOURCES:.c=.d)
+OBJECTS = $(SOURCES:.c=.o)
+HEADERS = \
+	dataentry.h \
+	devGNOME.h \
+	devGTK.h \
+	gdkrotated.h \
+	gnome-find-dialog.h \
+	gtkconsole.h \
+	terminal-functions.h \
+	terminal-menu.h \
+	terminal-prefs.h \
+	terminal-toolbar.h \
+	terminal.h
+
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+DISTFILES = Makefile.in $(SOURCES) $(HEADERS)
 
 LIB = libRgnome.a
 
@@ -45,13 +57,13 @@ Makefile: $(srcdir)/Makefile.in \
   ../include/Version.h \
   ../include/FFDecl.h \
   ../include/FFTab.h \
-  $(DEPS)
+  $(DEPENDS)
 	@cd $(top_builddir) && \
 	  CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= \
 	  $(SHELL) ./config.status
 
 Makedeps: Makefile
-	@cat $(DEPS) >> $<
+	@cat $(DEPENDS) >> $<
 	@touch $@
 
 R: Makefile
@@ -63,8 +75,8 @@ R: Makefile
 ../include/FFDecl.h ../include/FFTab.h: $(top_srcdir)/src/appl/ROUTINES
 	(cd ../include; $(top_srcdir)/tools/GETSYMBOLS)
 
-$(LIB): $(OBJS)
-	$(AR) cr $(LIB) $(OBJS)
+$(LIB): $(OBJECTS)
+	$(AR) cr $(LIB) $(OBJECTS)
 	$(RANLIB) $(LIB)
 
 mostlyclean: clean
diff --git a/src/include/Makefile.in b/src/include/Makefile.in
index b8e55703435..6a38ec769cb 100644
--- a/src/include/Makefile.in
+++ b/src/include/Makefile.in
@@ -10,15 +10,18 @@ subdir = src/include
 
 include $(top_builddir)/Makeconf
 
-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir) \
-	  && ls Makefile.in Platform.h.in Version.h.in *.h)
-
-SRC_HEADERS = S.h S_compat.h f2c.h Arith.h Complex.h Error.h Errormsg.h \
-	 Fortran.h Applic.h Blas.h Linpack.h Mathlib.h Memory.h PrtUtil.h \
-	 Random.h Rdefines.h Rinternals.h Utils.h
+SRC_HEADERS = Applic.h Arith.h Blas.h Complex.h Error.h Errormsg.h \
+	Fortran.h Linpack.h Mathlib.h Memory.h PrtUtil.h Random.h \
+	Rdefines.h Rinternals.h S.h S_compat.h Utils.h f2c.h
 OBJ_HEADERS = Platform.h Version.h
 
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+DISTFILES = Makefile.in README \
+	Defn.h Fileio.h Graphics.h IOStuff.h Parse.h Print.h \
+	Statdecl.h Stattab.h \
+	$(SRC_HEADERS) \
+	Platform.h.in Version.h.in
+
 all: Makefile R
 
 Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
diff --git a/src/main/Makefile.in b/src/main/Makefile.in
index bb78abb1c3b..36d6ee02211 100644
--- a/src/main/Makefile.in
+++ b/src/main/Makefile.in
@@ -10,10 +10,7 @@ subdir = src/main
 
 include $(top_builddir)/Makeconf
 
-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir) && ls Makefile.in *.[cfhy])
-
-SRCS = \
+SOURCES = \
 	arithmetic.c \
 	array.c \
 	attrib.c \
@@ -77,8 +74,11 @@ SRCS = \
 	unique.c \
 	util.c \
 	version.c
-DEPS = $(SRCS:.c=.d)
-OBJS = $(SRCS:.c=.o)
+DEPENDS = $(SOURCES:.c=.d)
+OBJECTS = $(SOURCES:.c=.o)
+
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+DISTFILES = $(SOURCES) arithmetic.h names.h gram.y
 
 RLIBS = ../unix/libunix.a ../appl/libappl.a ../nmath/libmath.a
 RGNOMELIBS = ../gnome/libRgnome.a ../appl/libappl.a ../nmath/libmath.a
@@ -94,13 +94,13 @@ Makefile: $(srcdir)/Makefile.in \
   ../include/Platform.h \
   ../include/Version.h \
   ../include/FFDecl.h \
-  $(DEPS)
+  $(DEPENDS)
 	@cd $(top_builddir) && \
 	  CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= \
 	  $(SHELL) ./config.status
 
 Makedeps: Makefile
-	@cat $(DEPS) >> Makefile
+	@cat $(DEPENDS) >> Makefile
 	@touch $@
 
 R: Makefile
@@ -115,16 +115,16 @@ R: Makefile
 ../include/FFDecl.h: $(top_srcdir)/src/appl/ROUTINES
 	(cd ../include; $(top_srcdir)/tools/GETSYMBOLS)
 
-$(top_builddir)/bin/R.X11: $(OBJS) $(RLIBS) @EXPORTFILE@
+$(top_builddir)/bin/R.X11: $(OBJECTS) $(RLIBS) @EXPORTFILE@
 	@$(MKINSTALLDIRS) $(top_builddir)/bin
-	$(LDCMD) $(DLLFLAGS) -o $@ $(OBJS) $(ALL_LIBS)
+	$(LDCMD) $(DLLFLAGS) -o $@ $(OBJECTS) $(ALL_LIBS)
 
-$(top_builddir)/bin/R.gnome: $(OBJS) $(RGNOMELIBS)
+$(top_builddir)/bin/R.gnome: $(OBJECTS) $(RGNOMELIBS)
 	@$(MKINSTALLDIRS) $(top_builddir)/bin
-	$(LDCMD) $(DLLFLAGS) $(GNOME_LIBDIR) -o $@ $(OBJS) $(ALL_GNOME_LIBS)
+	$(LDCMD) $(DLLFLAGS) $(GNOME_LIBDIR) -o $@ $(OBJECTS) $(ALL_GNOME_LIBS)
 
-$(top_builddir)/etc/R.exp: $(OBJS) $(RLIBS)
-	@$(top_srcdir)/tools/ldAIX4 -o $@ $(OBJS) $(RLIBS)
+$(top_builddir)/etc/R.exp: $(OBJECTS) $(RLIBS)
+	@$(top_srcdir)/tools/ldAIX4 -o $@ $(OBJECTS) $(RLIBS)
 
 ../unix/libunix.a:
 	(cd ../unix;  $(MAKE) $(@F))
@@ -134,8 +134,8 @@ $(top_builddir)/etc/R.exp: $(OBJS) $(RLIBS)
 	(cd ../nmath; $(MAKE) $(@F))
 
 gram.c: $(srcdir)/gram.y
-	$(YACC) $(srcdir)/gram.y
-	mv y.tab.c $@
+	$(YACC) $(YFLAGS) $(srcdir)/gram.y
+	$(top_srcdir)/tools/move-if-change y.tab.c $(@F)
 
 mostlyclean: clean
 clean:
diff --git a/src/nmath/Makefile.in b/src/nmath/Makefile.in
index 4b804c410b7..b39ae224b0d 100644
--- a/src/nmath/Makefile.in
+++ b/src/nmath/Makefile.in
@@ -6,14 +6,11 @@ srcdir = @srcdir@
 top_srcdir = @top_srcdir@
 
 top_builddir = ../..
-
-include $(top_builddir)/Makeconf
 subdir = src/nmath
 
-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir) && ls Makefile.in *.[cfh])
+include $(top_builddir)/Makeconf
 
-SRCS = \
+SOURCES = \
 	mlutils.c \
 	d1mach.c i1mach.c \
 	fmax2.c fmin2.c fmod.c fprec.c fround.c ftrunc.c \
@@ -47,28 +44,31 @@ SRCS = \
 	ptukey.c qtukey.c \
 	wilcox.c \
 	signrank.c
-DEPS = $(SRCS:.c=.d)
-OBJS = $(SRCS:.c=.o)
+DEPENDS = $(SOURCES:.c=.d)
+OBJECTS = $(SOURCES:.c=.o)
+
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+DISTFILES = Makefile.in $(SOURCES)
 
 LIB = libmath.a
 
 all: Makefile Makedeps R
 
-Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status $(DEPS)
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status $(DEPENDS)
 	@cd $(top_builddir) && \
 	  CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= \
 	  $(SHELL) ./config.status
 
 Makedeps: Makefile
-	@cat $(DEPS) >> Makefile
+	@cat $(DEPENDS) >> Makefile
 	@touch $@
 
 R: Makefile
 	@$(MAKE) Makedeps
 	@$(MAKE) $(LIB)
 
-$(LIB): $(OBJS)
-	$(AR) cr $(LIB) $(OBJS)
+$(LIB): $(OBJECTS)
+	$(AR) cr $(LIB) $(OBJECTS)
 	$(RANLIB) $(LIB)
 
 mostlyclean: clean
diff --git a/src/scripts/Makefile.in b/src/scripts/Makefile.in
index f40f9b4146a..d50ccbca260 100644
--- a/src/scripts/Makefile.in
+++ b/src/scripts/Makefile.in
@@ -10,13 +10,15 @@ subdir = src/scripts
 
 include $(top_builddir)/Makeconf
 
-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir) && ls | sed '/CVS/d')
-
-SRC_SCRIPTS = BATCH Rd2dvi check filename help help.links \
+SCRIPTS_S = BATCH Rd2dvi check filename help help.links \
 	massage-Examples pager
-OBJ_SCRIPTS = COMPILE INSTALL REMOVE Rd2contents Rd2txt Rdconv Rdindex \
-	Rman2Rd SHLIB Sd2Rd build-help fwf2table help.pretty html2dos 
+SCRIPTS_B_IN = COMPILE.in INSTALL.in REMOVE.in Rd2contents.in Rd2txt.in \
+	Rdconv.in Rdindex.in Rman2Rd.in SHLIB.in Sd2Rd.in build-help.in \
+	fwf2table.in help.pretty.in html2dos.in
+SCRIPTS_B = $(SCRIPTS_B_IN:.in=)
+
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+DISTFILES = Makefile.in $(SCRIPTS_S) $(SCRIPTS_B_IN) R.sh.in
 
 all: Makefile R
 
@@ -25,22 +27,27 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 	  CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= \
 	  $(SHELL) ./config.status
 
-R:
+R: $(SCRIPTS_B) R.sh
 	@$(MKINSTALLDIRS) $(top_builddir)/bin
 	@cat R.sh | \
 	  (cd $(top_builddir); sed "s@R_HOME_DIR*@`pwd`@" > bin/R)
 	@chmod +x $(top_builddir)/bin/R
-	@for f in $(SRC_SCRIPTS); do \
+	@for f in $(SCRIPTS_S); do \
 	  $(INSTALL) $(srcdir)/$$f $(top_builddir)/bin; \
 	done
-	@for f in $(OBJ_SCRIPTS); do \
+	@for f in $(SCRIPTS_B); do \
 	  $(INSTALL) $$f $(top_builddir)/bin; \
 	done
 
+%: %.in $(top_builddir)/config.status
+	cd $(top_builddir) && \
+	  CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= \
+	  $(SHELL) ./config.status
+
 mostlyclean: clean
 clean:
 distclean:
-	@rm -f Makefile R.sh $(OBJ_SCRIPTS)
+	@rm -f Makefile R.sh $(SCRIPTS_B)
 maintainer-clean: distclean
 
 distdir: $(DISTFILES)
diff --git a/src/unix/Makefile.in b/src/unix/Makefile.in
index 5fe365f9e05..1eeedf53d20 100644
--- a/src/unix/Makefile.in
+++ b/src/unix/Makefile.in
@@ -12,22 +12,14 @@ include $(top_builddir)/Makeconf
 
 ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(X_CFLAGS) $(CPPFLAGS) $(DEFS)
 
+SOURCES = Rsock.c dataentry.c devPS.c devPicTeX.c devX11.c dynload.c \
+	edit.c rotated.c system.c sock.c
+DEPENDS = $(SOURCES:.c=.d)
+OBJECTS = $(SOURCES:.c=.o)
+HEADERS = Rsock.h dataentry.h devX11.h rotated.h sock.h
+
 distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir) && ls PSPAPER Makefile.in *.[cfh])
-
-SRCS = \
-	dataentry.c \
-	devPS.c \
-	devPicTeX.c \
-	devX11.c \
-	dynload.c \
-	edit.c \
-	rotated.c \
-	system.c \
-	Rsock.c \
-	sock.c
-DEPS = $(SRCS:.c=.d)
-OBJS = $(SRCS:.c=.o)
+DISTFILES = Makefile.in PSPAPER $(SOURCES) $(HEADERS)
 
 LIB = libunix.a
 
@@ -38,13 +30,13 @@ Makefile: $(srcdir)/Makefile.in \
   ../include/Version.h \
   ../include/FFDecl.h \
   ../include/FFTab.h \
-  $(DEPS)
+  $(DEPENDS)
 	@cd $(top_builddir) && \
 	  CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= \
 	  $(SHELL) ./config.status
 
 Makedeps: Makefile
-	@cat $(DEPS) >> Makefile
+	@cat $(DEPENDS) >> Makefile
 	@touch $@
 
 R: Makefile
@@ -56,8 +48,8 @@ R: Makefile
 ../include/FFDecl.h ../include/FFTab.h: $(top_srcdir)/src/appl/ROUTINES
 	(cd ../include; $(top_srcdir)/tools/GETSYMBOLS)
 
-$(LIB): $(OBJS)
-	$(AR) cr $(LIB) $(OBJS)
+$(LIB): $(OBJECTS)
+	$(AR) cr $(LIB) $(OBJECTS)
 	$(RANLIB) $(LIB)
 
 mostlyclean: clean
diff --git a/tests/Makefile.in b/tests/Makefile.in
index a55c2c7bccd..f7bc09f2518 100644
--- a/tests/Makefile.in
+++ b/tests/Makefile.in
@@ -10,18 +10,19 @@ subdir = tests
 
 include $(top_builddir)/Makeconf
 
-distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
-DISTFILES = $(shell cd $(srcdir); \
-	       ls Makefile.in README Rdiff *.R *.Rout.save)
 SUBDIRS = Examples
 
 R = LC_ALL=C $(top_builddir)/bin/R --vanilla
 
 TESTsrc = simple-true.R arith-true.R arith.R d-p-q-r-tests.R \
 	 print-tests.R is-things.R primitive-funs.R eval-etc.R
-
 TESTout = $(TESTsrc:.R=.Rout)
 
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+DISTFILES = Makefile.in README Rdiff \
+	all-equal.R mode-methods.R $(TESTsrc) \
+	$(TESTsrc:.R=.Rout.save)
+
 %.Rout: %.R stamp-R
 	@rm -f $@.fail
 	@(SRCDIR=$(srcdir); export SRCDIR; \