kmer/Make.rules   |  4 ++--
 kmer/configure.sh | 20 +++++++++----------
 src/c_make.as     | 58 +++++++++++++++++++++++++++----------------------------
 src/c_make.gen    |  4 ++--
 4 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/kmer/Make.rules b/kmer/Make.rules
index f904b13..5c2d477 100644
--- a/kmer/Make.rules
+++ b/kmer/Make.rules
@@ -139,12 +139,12 @@ ${ALL_CXX_DEPS}:%.d:%
 ## EXE targets
 ALL_C_EXES   :=$(strip $(foreach x,${//},${${x:.=.C_EXES}}))
 ${ALL_C_EXES}:
-	${-CC} ${CLD} ${CLDFLAGS} -o $@ $+ ${CLIBS}
+	${-CC} ${CLD} ${CLDFLAGS} ${LDFLAGS} -o $@ $+ ${CLIBS}
 __SUBGOALS__+=$${${1:.=.C_EXES}}
 
 ALL_CXX_EXES :=$(strip $(foreach x,${//},${${x:.=.CXX_EXES}}))
 ${ALL_CXX_EXES}:
-	${-CXX} ${CXXLD} ${CXXLDFLAGS} -o $@ $+ ${CXXLIBS}
+	${-CXX} ${CXXLD} ${CXXLDFLAGS} ${LDFLAGS} -o $@ $+ ${CXXLIBS}
 __SUBGOALS__+=$${${1:.=.CXX_EXES}}
 
 define .RULE-install-copy-C-CXX-EXES
diff --git a/kmer/configure.sh b/kmer/configure.sh
index 2f0d5ea..9daf89f 100755
--- a/kmer/configure.sh
+++ b/kmer/configure.sh
@@ -254,13 +254,13 @@ EOF
 # -*- makefile -*-
 #  Linux, optimized
 CC                := $CC
-SHLIB_FLAGS       := -shared
-CFLAGS_COMPILE    := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
-CLDFLAGS          := -L/usr/local/lib
+SHLIB_FLAGS       := -shared ${LDFLAGS}
+CFLAGS_COMPILE    := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
+CLDFLAGS          := 
 CLIBS             := -pthread -ldl
 CXX               := $CXX
-CXXFLAGS_COMPILE  := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
-CXXLDFLAGS        := -L/usr/local/lib
+CXXFLAGS_COMPILE  := -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
+CXXLDFLAGS        := 
 CXXLIBS           := -pthread -ldl
 ARFLAGS           := ruvs
 INSTALL/          := $target/
@@ -272,13 +272,13 @@ EOF
 # -*- makefile -*-
 #  Linux64, optimized
 CC                := $CC
-SHLIB_FLAGS       := -shared
-CFLAGS_COMPILE    := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
-CLDFLAGS          := -L/usr/local/lib
+SHLIB_FLAGS       := -shared ${LDFLAGS}
+CFLAGS_COMPILE    := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
+CLDFLAGS          := 
 CLIBS             := -pthread -ldl
 CXX               := $CXX
-CXXFLAGS_COMPILE  := -m64 -fPIC -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
-CXXLDFLAGS        := -L/usr/local/lib
+CXXFLAGS_COMPILE  := -fPIC -D_REENTRANT -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts
+CXXLDFLAGS        := 
 CXXLIBS           := -pthread -ldl
 ARFLAGS           := ruvs
 INSTALL/          := $target/
diff --git a/src/c_make.as b/src/c_make.as
index 0172807..4304589 100644
--- a/src/c_make.as
+++ b/src/c_make.as
@@ -64,27 +64,27 @@ include $(LOCAL_WORK)/src/c_make.gen
 
 ifeq ($(OSTYPE), Linux)
   ifeq ($(MACHINETYPE), i686)
-    ARCH_LDFLAGS  += -pthread -lm
-    ARCH_CFLAGS   += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
+    LINK_LIBS  += -pthread -lm
+    ARCH_CFLAGS   += -pthread -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
     ARCH_LIB       = /usr/X11R6/lib
   endif
   ifeq ($(MACHINETYPE), amd64)
-    ARCH_LDFLAGS  += -pthread -lm
-    ARCH_CFLAGS   += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
+    LINK_LIBS  += -pthread -lm
+    ARCH_CFLAGS   += -pthread -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DX86_GCC_LINUX
     ARCH_LIB       = /usr/lib64 /usr/X11R6/lib64
   endif
   ifeq ($(MACHINETYPE), ia64)
-    ARCH_LDFLAGS  += -pthread -lm
-    ARCH_CFLAGS   += -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
+    LINK_LIBS  += -pthread -lm
+    ARCH_CFLAGS   += -pthread -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
     ARCH_LIB       = /usr/X11R6/lib
   endif
 
   ifeq ($(BUILDDEBUG), 1)
-    ARCH_CFLAGS  += -g 
-    ARCH_LDFLAGS +=
+    ARCH_CFLAGS  +=  
+    LINK_LIBS +=
   else
-    ARCH_CFLAGS  += -O2
-    ARCH_LDFLAGS += -Wl,-O1
+    ARCH_CFLAGS  += 
+    LINK_LIBS += 
   endif
 endif
 
@@ -94,19 +94,19 @@ endif
 
 ifeq ($(OSTYPE), FreeBSD)
   ifeq ($(MACHINETYPE), i386)
-    ARCH_LDFLAGS    += -pthread -lthr -lm
-    ARCH_CFLAGS      = -pthread -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
-    ARCH_CFLAGS      = -pthread       -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
+    LINK_LIBS    += -pthread -lthr -lm
+    ARCH_CFLAGS      = -pthread -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
+    ARCH_CFLAGS      = -pthread        -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare
   endif
   ifeq ($(MACHINETYPE), amd64)
-    ARCH_LDFLAGS    += -pthread -lthr -lm
-    ARCH_CFLAGS      =  -pthread               -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
-    ARCH_CFLAGS      =  -pthread -Wall -Wextra -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
+    LINK_LIBS    += -pthread -lthr -lm
+    ARCH_CFLAGS      =  -pthread                -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
+    ARCH_CFLAGS      =  -pthread -Wall -Wextra  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat
   endif
 
   ifeq ($(BUILDCOVERAGE), 1)
     ARCH_CFLAGS   += -g -fprofile-arcs -ftest-coverage
-    ARCH_LDFLAGS  += -lgcov
+    LINK_LIBS  += -lgcov
   else
     ifeq ($(BUILDDEBUG), 1)
       ARCH_CFLAGS   += -g
@@ -140,14 +140,14 @@ ifeq ($(OSTYPE), Darwin)
 
   ifeq ($(MACHINETYPE), i386)
     ifeq ($(BUILDDEBUG), 1)
-      ARCH_CFLAGS   += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
-      ARCH_LDFLAGS  += -m64 -lm
+      ARCH_CFLAGS   += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE -Wall  -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -g
+      LINK_LIBS  += -m64 -lm
     else
 #  Wow, -Wshorten-64-to-32  is tough
-      ARCH_CFLAGS   += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE       -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
+      ARCH_CFLAGS   += -fPIC -m64 -fmessage-length=0 -D_THREAD_SAFE        -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -fast
 #     ARCH_CFLAGS   += -Wextra
 #     ARCH_CFLAGS   += -pedantic  (see above about pedantic)
-      ARCH_LDFLAGS  += -m64 -lm
+      LINK_LIBS  += -m64 -lm
     endif
   endif
 
@@ -161,23 +161,23 @@ endif
 ifeq ($(OSTYPE), SunOS)
   ifeq ($(MACHINETYPE), i86pc)
     ARCH_CFLAGS    = -DBYTE_ORDER=LITTLE_ENDIAN -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
-    ARCH_LDFLAGS  += -lm
+    LINK_LIBS  += -lm
   endif
 
   ifeq ($(MACHINETYPE), sparc32)
     ARCH_CFLAGS    = -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
-    ARCH_LDFLAGS  += -lm -lnsl -lsocket
+    LINK_LIBS  += -lm -lnsl -lsocket
   endif
 
   ifeq ($(MACHINETYPE), sparc64)
     ARCH_CFLAGS    = -m64 -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -pthreads
-    ARCH_LDFLAGS  += -m64 -lm -lnsl -lsocket
+    LINK_LIBS  += -lm -lnsl -lsocket
   endif
 
   ifeq ($(BUILDDEBUG), 1)
-    ARCH_CFLAGS   += -g
+    ARCH_CFLAGS   +=
   else
-    ARCH_CFLAGS   += -O
+    ARCH_CFLAGS   +=
   endif
 endif
 
@@ -186,14 +186,14 @@ endif
 
 ifeq ($(BUILDPROFILE), 1)
   ARCH_CFLAGS  += -pg
-  ARCH_LDFLAGS += -pg
+  LINK_LIBS += -pg
 endif
 
 # One can argue that CXXFLAGS should be separate.  For now, we only
 # add to the flags.
 
 CFLAGS          += $(ARCH_CFLAGS)
-CXXFLAGS        += $(ARCH_CFLAGS) $(ARCH_CXXFLAGS)
+CXXFLAGS        += $(ARCH_CXXFLAGS)
 LDFLAGS         += $(ARCH_LDFLAGS)
 
 INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
@@ -205,7 +205,7 @@ LIB_IMPORT_DIRS += $(ARCH_LIB)
 OBJ_SEARCH_PATH  = $(LOCAL_OBJ)
 
 ifeq ($(SITE_NAME), JCVI)
-  LDFLAGS += -lcurl
+  LINK_LIBS += -lcurl
 endif
 
 #  The order of compilation here is very carefully chosen to be the
diff --git a/src/c_make.gen b/src/c_make.gen
index 7b5227c..c27b777 100644
--- a/src/c_make.gen
+++ b/src/c_make.gen
@@ -396,12 +396,12 @@ $(LIBRARIES):
 $(C_PROGS):
 	@ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
 	cd $(LOCAL_OBJ); \
-	  $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
+	  $(CC) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
 
 $(CXX_PROGS):
 	@ echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";
 	cd $(LOCAL_OBJ); \
-          $(CXX) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LDFLAGS)
+          $(CXX) $(LDFLAGS) -o $(LOCAL_BIN)/$(notdir $@) $(filter-out lib%.a, $+) $(patsubst lib%.a, -l%, $(filter lib%.a, $+)) $(LD_DIRS) $(LINK_LIBS)
 
 $(SCRIPT_PROGS): %.sh:
 	@echo "++++++++++++++++++++ " $@ "++++++++++++++++++++++";