Make build system respect user flags

--- a/makefile
+++ b/makefile
@@ -1,6 +1,5 @@
-CXXFLAGS = -O3
 all:
-	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
+	$(MAKE) -C src
 
 prefix = /usr/local
 exec_prefix = $(prefix)
@@ -10,15 +9,15 @@
 	cp src/last?? scripts/*.?? $(bindir)
 
 clean:
-	@cd src && $(MAKE) clean
+	$(MAKE) -C src clean
 
 html:
-	@cd doc && $(MAKE)
+	$(MAKE) -C doc
 
 distdir = last-`hg id -n`
 
 dist: log html
-	@cd src && $(MAKE) version.hh
+	$(MAKE) -C src version.hh
 	rsync -rC --exclude 'last??' doc examples makefile s* *.txt $(distdir)
 	zip -qrm $(distdir) $(distdir)
 
--- a/src/makefile
+++ b/src/makefile
@@ -1,12 +1,9 @@
-CXX = g++
-CC  = gcc
-
-CXXFLAGS = -O3 -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
--Wcast-align -Wno-long-long -ansi -pedantic
+last_CXXFLAGS = -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef	\
+-Wcast-align -Wno-long-long -pedantic
 # -Wconversion
 # -fomit-frame-pointer ?
 
-CFLAGS = -Wall
+last_CFLAGS = -Wall
 
 DBSRC = Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc	\
 SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc	\
@@ -49,17 +46,20 @@
 
 all: lastdb lastal lastex
 
+.cpp.o:
+	$(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) -c -o $@ $<
+
 lastdb: $(DBSRC) $(DBINC) makefile
-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC)
+	$(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(DBSRC)
 
 lastal: $(ALSRC) $(ALINC) makefile $(OBJ)
-	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ)
+	$(CXX) $(CPPFLAGS) $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(ALSRC) $(OBJ)
 
 lastex: $(EXSRC) $(EXINC) makefile
-	$(CXX) -Igumbel_params $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC)
+	$(CXX) $(CPPFLAGS) -Igumbel_params $(last_CXXFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(EXSRC)
 
 $(OBJ): CA_code/*.c CA_code/*.h makefile
-	$(CC) $(CPPFLAGS) $(CFLAGS) -c CA_code/lambda_calculator.c
+	$(CC) $(CPPFLAGS) $(last_CFLAGS) $(CFLAGS) -c -o $@ CA_code/lambda_calculator.c
 
 clean:
 	rm -f lastdb lastal lastex $(OBJ)