Fix build system to restore some sanity

--- a/Makefile
+++ b/Makefile
@@ -27,31 +27,27 @@
 
 
 TOP_DIR     := $(CURDIR)
-BIN_DIR     := $(TOP_DIR)
-AUX_BIN_DIR := $(TOP_DIR)/aux_bin
+
+BIN_DIR     = $(EPREFIX)/usr/bin
+SCRIPT_DIR  = $(EPREFIX)/usr/share/mummer/scripts
+AUX_BIN_DIR = $(EPREFIX)/usr/bin
 
 DOC_DIR       := $(TOP_DIR)/docs
 SCRIPT_DIR    := $(TOP_DIR)/scripts
 TIGR_SRC_DIR  := $(TOP_DIR)/src/tigr
 KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
 
-CC   := $(filter /%,$(shell /bin/sh -c 'type gcc'))
-CXX  := $(filter /%,$(shell /bin/sh -c 'type g++'))
 SED  := $(filter /%,$(shell /bin/sh -c 'type sed'))
 CSH  := $(filter /%,$(shell /bin/sh -c 'type csh'))
 PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
-AR   := $(filter /%,$(shell /bin/sh -c 'type ar'))
 
-CXXFLAGS = -O3
-CFLAGS = -O3
-LDFLAGS  =
 
 FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog
 
 
 
 #-- EXPORT THESE VARIABLES TO OTHER MAKEFILES
-export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
+export BIN_DIR SCRIPT_DIR AUX_BIN_DIR
 
 
 
@@ -114,15 +110,15 @@
 
 
 kurtz:
-	cd $(KURTZ_SRC_DIR); $(MAKE) mummer
+	$(MAKE) -C $(KURTZ_SRC_DIR) mummer
 
 
 scripts:
-	cd $(SCRIPT_DIR); $(MAKE) all
+	$(MAKE) -C $(SCRIPT_DIR) all
 
 
 tigr:
-	cd $(TIGR_SRC_DIR); $(MAKE) all
+	$(MAKE) -C $(TIGR_SRC_DIR) all
 
 
 uninstall: clean
--- a/scripts/Makefile
+++ b/scripts/Makefile
@@ -1,21 +1,10 @@
-#-- Imported variables from top level makefile
-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
+BIN_DIR     = $(EPREFIX)/usr/bin
+SCRIPT_DIR  = $(EPREFIX)/usr/share/mummer/scripts
+AUX_BIN_DIR = $(EPREFIX)/usr/bin
 
-ifndef BIN_DIR
-BIN_DIR := $(CURDIR)
-endif
-ifndef AUX_BIN_DIR
-AUX_BIN_DIR := $(CURDIR)
-endif
-ifndef SCRIPT_DIR
-SCRIPT_DIR := $(CURDIR)
-endif
-
-SCRIPT_DIR := $(CURDIR)
 SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
 CSH := $(filter /%,$(shell /bin/sh -c 'type csh'))
 PERL := $(filter /%,$(shell /bin/sh -c 'type perl'))
-VPATH := $(BIN_DIR)
 
 ALL := exact-tandems mapview mummerplot nucmer promer \
        run-mummer1 run-mummer3 nucmer2xfig dnadiff
@@ -39,58 +28,49 @@
 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
 		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
-		exact-tandems.csh > $(BIN_DIR)/exact-tandems
-	chmod 755 $(BIN_DIR)/exact-tandems
+		exact-tandems.csh > exact-tandems
 
 mapview: mapview.pl
 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
 		-e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
-                mapview.pl > $(BIN_DIR)/mapview
-	chmod 755 $(BIN_DIR)/mapview
+                mapview.pl > mapview
 
 mummerplot: mummerplot.pl Foundation.pm
 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
-                mummerplot.pl > $(BIN_DIR)/mummerplot
-	chmod 755 $(BIN_DIR)/mummerplot
+                mummerplot.pl > mummerplot
 
 dnadiff: dnadiff.pl Foundation.pm
 	$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
                -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
                -e 's?__BIN_DIR?$(BIN_DIR)?g' \
-                 dnadiff.pl > $(BIN_DIR)/dnadiff
-	chmod 755 $(BIN_DIR)/dnadiff
+                 dnadiff.pl > dnadiff
 
 nucmer: nucmer.pl Foundation.pm
 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
                 -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
-                 nucmer.pl > $(BIN_DIR)/nucmer
-	chmod 755 $(BIN_DIR)/nucmer
+                 nucmer.pl > nucmer
 
 promer: promer.pl Foundation.pm
 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
                 -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
                 -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
                 -e 's?__BIN_DIR?$(BIN_DIR)?g' \
-                promer.pl > $(BIN_DIR)/promer
-	chmod 755 $(BIN_DIR)/promer
+                promer.pl > promer
 
 run-mummer1: run-mummer1.csh
 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
-		run-mummer1.csh > $(BIN_DIR)/run-mummer1
-	chmod 755 $(BIN_DIR)/run-mummer1
+		run-mummer1.csh > run-mummer1
 
 run-mummer3: run-mummer3.csh
 	$(SED)  -e 's?__CSH_PATH?$(CSH)?g' \
 		-e 's?__BIN_DIR?$(BIN_DIR)?g' \
-		run-mummer3.csh > $(BIN_DIR)/run-mummer3
-	chmod 755 $(BIN_DIR)/run-mummer3
+		run-mummer3.csh > run-mummer3
 
 nucmer2xfig: nucmer2xfig.pl
 	$(SED)  -e 's?__PERL_PATH?$(PERL)?g' \
-		nucmer2xfig.pl > $(BIN_DIR)/nucmer2xfig
-	chmod 755 $(BIN_DIR)/nucmer2xfig
+		nucmer2xfig.pl > nucmer2xfig
--- a/src/kurtz/libbasedir/Makefile
+++ b/src/kurtz/libbasedir/Makefile
@@ -5,8 +5,6 @@
 
 SPLINTFLAGS=-f ../Splintoptions -DDEBUG
 
-LD=$(CC)
-
 ##CFLAGS=${DEFINECFLAGS}
 
 LIBBASE=libbase.a
@@ -24,14 +22,14 @@
 
 
 $(LIBBASE): $(LIBOBJECTS)
-	ar sruv $@ $(LIBOBJECTS)
+	$(AR) sruv $@ $(LIBOBJECTS)
 
 
 include Filegoals.mf
 
 
 $(LIBBASEDBG): $(LIBDEBUGOBJECTS)
-	ar sruv $@ $(LIBDEBUGOBJECTS)
+	$(AR) sruv $@ $(LIBDEBUGOBJECTS)
 
 
 .PHONY:clean
--- a/src/kurtz/Makefile
+++ b/src/kurtz/Makefile
@@ -1,7 +1,7 @@
 all:
-	cd libbasedir; $(MAKE) all
-	cd streesrc; $(MAKE) all
-	cd mm3src; $(MAKE) all
+	$(MAKE) -C libbasedir all
+	$(MAKE) -C streesrc all
+	$(MAKE) -C mm3src all
 
 clean:
 	rm -f *~
@@ -10,11 +10,11 @@
 	cd mm3src; $(MAKE) clean
 
 mummer:
-	cd libbasedir; $(MAKE) libbase.a
-	cd streesrc; $(MAKE) libstree.a
-	cd mm3src; $(MAKE) mummer
+	$(MAKE) -C libbasedir libbase.a
+	$(MAKE) -C streesrc libstree.a
+	$(MAKE) -C mm3src mummer
 
 splintall:
-	cd libbasedir; ${MAKE} splintall
-	cd streesrc; ${MAKE} splintall
-	cd mm3src; ${MAKE} splintall
+	$(MAKE) -C libbasedir splintall
+	$(MAKE) -C streesrc splintall
+	$(MAKE) -C mm3src splintall
--- a/src/kurtz/mm3src/Makefile
+++ b/src/kurtz/mm3src/Makefile
@@ -3,11 +3,7 @@
 
 ##include ../Makedef
 
-ifndef BIN_DIR
-BIN_DIR := $(CURDIR)
-endif
-
-VPATH := $(BIN_DIR)
+BIN_DIR     = $(EPREFIX)/usr/bin
 
 ALL := maxmat3.x maxmat3.dbg.x
 
@@ -15,11 +11,8 @@
 LIBSTREEDIR=../streesrc
 INCLUDEDIR=-I${LIBBASEDIR} -I${LIBSTREEDIR}
 
-override CFLAGS+=$(INCLUDEDIR)
-##CFLAGS=${DEFINECFLAGS} $(INCLUDEDIR)
-##LDFLAGS=${DEFINELDFLAGS}
+override CPPFLAGS+=$(INCLUDEDIR)
 SPLINTFLAGS=${INCLUDEDIR} -f ../Splintoptions -DDEBUG
-LD=$(CC)
 
 LIBBASE=$(LIBBASEDIR)/libbase.a
 LIBBASEDBG=$(LIBBASEDIR)/libbase.dbg.a
@@ -40,16 +33,16 @@
 all: $(ALL)
 
 mummer: $(MUM3OBJECTS) $(LIBSTREE)
-	$(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
-	-o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
+	$(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
+	-o $@
 
 maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE)
-	$(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
-	-o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
+	$(CC) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
+	-o $@
 
 maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG)
-	$(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
-	-lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
+	$(CC) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
+	-lm -o $@
 
 include Filegoals.mf
 
--- a/src/kurtz/streesrc/Makefile
+++ b/src/kurtz/streesrc/Makefile
@@ -23,8 +23,6 @@
 
 #-DSTARTFACTOR=0.5
 
-LD=${CC}
-
 LIBBASE=${LIBBASEDIR}/libbase.a
 LIBBASEDBG=${LIBBASEDIR}/libbase.dbg.a
 
@@ -65,29 +63,29 @@
 include Filegoals.mf
 
 libstree.4.a: $(OBJECTS4)
-	ar sruv $@ $(OBJECTS4)
+	$(AR) sruv $@ $(OBJECTS4)
 
 libstree.a: $(OBJECTS)
-	ar sruv $@ $(OBJECTS)
+	$(AR) sruv $@ $(OBJECTS)
 
 libstree.dbg.4.a: $(DBGOBJECTS4)
-	ar sruv $@ $(DBGOBJECTS4)
+	$(AR) sruv $@ $(DBGOBJECTS4)
 
 libstree.dbg.a: $(DBGOBJECTS)
-	ar sruv $@ $(DBGOBJECTS)
+	$(AR) sruv $@ $(DBGOBJECTS)
 
 
 stree.x: stree.o libstree.a
-	$(LD) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@
+	$(CC) $(LDFLAGS) stree.o libstree.a $(LIBBASE) -o $@
 
 loc.x: loc.o libstree.a
-	$(LD) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@
+	$(CC) $(LDFLAGS) loc.o libstree.a $(LIBBASE) -o $@
 
 stree.dbg.x: stree.dbg.o libstree.dbg.a 
-	$(LD) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
+	$(CC) $(LDFLAGS) stree.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
 
 loc.dbg.x: loc.dbg.o libstree.dbg.a 
-	$(LD) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
+	$(CC) $(LDFLAGS) loc.dbg.o libstree.dbg.a $(LIBBASEDBG) -o $@
 
 streeproto.h: $(PROTOFILES) Mkstreeproto.sh
 	@echo "make $@"
--- a/src/tigr/Makefile
+++ b/src/tigr/Makefile
@@ -1,20 +1,3 @@
-#-- Imported variables from top level makefile
-# BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
-
-ifndef BIN_DIR
-BIN_DIR := $(CURDIR)
-endif
-ifndef AUX_BIN_DIR
-AUX_BIN_DIR := $(CURDIR)
-endif
-
-OBJ_RULE = $(CXX) $(CXXFLAGS) $< -c -o $@
-BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(BIN_DIR)/$@; \
-           chmod 755 $(BIN_DIR)/$@
-AUX_BIN_RULE = $(CXX) $(CXXFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
-           chmod 755 $(AUX_BIN_DIR)/$@
-VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
-
 ALL := annotate combineMUMs delta-filter gaps mgaps \
      postnuc postpro prenuc prepro repeat-match \
      show-aligns show-coords show-tiling show-snps \
@@ -38,59 +21,22 @@
 
 #-- not so PHONY rules --#
 delta.o: delta.cc delta.hh
-	$(OBJ_RULE)
-
 tigrinc.o: tigrinc.cc tigrinc.hh
-	$(OBJ_RULE)
-
 sw_align.o: sw_align.cc sw_align.hh tigrinc.hh
-	$(OBJ_RULE)
-
 translate.o: translate.cc translate.hh
-	$(OBJ_RULE)
-
 
 annotate: annotate.cc tigrinc.o
-	$(BIN_RULE)
-
 combineMUMs: combineMUMs.cc tigrinc.o
-	$(BIN_RULE)
-
 delta-filter: delta-filter.cc tigrinc.o delta.o
-	$(BIN_RULE)
-
 gaps: gaps.cc tigrinc.o
-	$(BIN_RULE)
-
 mgaps: mgaps.cc tigrinc.o
-	$(BIN_RULE)
-
 postnuc: postnuc.cc tigrinc.o sw_align.o
-	$(AUX_BIN_RULE)
-
 postpro: postpro.cc tigrinc.o sw_align.o translate.o
-	$(AUX_BIN_RULE)
-
 prenuc: prenuc.cc tigrinc.o
-	$(AUX_BIN_RULE)
-
 prepro: prepro.cc tigrinc.o translate.o
-	$(AUX_BIN_RULE)
-
 repeat-match: repeat-match.cc tigrinc.o
-	$(BIN_RULE)
-
 show-aligns: show-aligns.cc tigrinc.o translate.o delta.o
-	$(BIN_RULE)
-
 show-coords: show-coords.cc tigrinc.o delta.o
-	$(BIN_RULE)
-
 show-tiling: show-tiling.cc tigrinc.o delta.o
-	$(BIN_RULE)
-
 show-snps: show-snps.cc tigrinc.o translate.o delta.o
-	$(BIN_RULE)
-
 show-diff: show-diff.cc tigrinc.o delta.o
-	$(BIN_RULE)