Make build system semi-sane:
* Respect CC, CXX, CFLAGS, CXXFLAGS, CPPFLAGS, LDFLAGS and LIBS
* Remove default optimisation flags
* Remove -fpermissive from DEFS (as source builds fine now)
* Add large file support (LFS) via CPPFLAGS and not in Makefile

--- a/makefile
+++ b/makefile
@@ -47,23 +47,20 @@
 #
 # compilation
 #
-CXX= g++
-KRCC= gcc
-CC=gcc 
+CXX ?= g++
+CC ?= gcc 
 
 #
 #
-CFLGS= -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64 -DSAMTOOLS_AVAILABLE
+DEFS = -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -DSAMTOOLS_AVAILABLE
 
-OPT= -O
 #
 # Include directory for template classes must be included
 # in both compilation & link lines, even if .h file is
 # found in default path.  C front, gotta love it.
 #
-INC=  -I/usr/X11R6/include -I/me1/gordon/samtools/samtools-0.1.18
+INCLUDES = $(SAMTOOLS_CPPFLAGS)
 
-DEPENDENCIES=
 #
 #
 # Linking
@@ -80,12 +77,9 @@
 #         /lib/ld-linux.so.2 (0x003ee000)
 # 
 # To fix cut/paste bug, I've made X11 always dynamic.
-CLIBS= -lX11
-LPATH= -L/usr/X11R6/lib
-ARCHIVES= /usr/X11R6/lib/libXm.a \
-/usr/X11R6/lib/libXt.a /usr/X11R6/lib/libSM.a \
-/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \
-/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a
+
+MOTIF_LIBS ?= -lXm -lXt
+ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS)
 
 
 
@@ -94,7 +88,6 @@
 #
 #LDFLGS=	-g
 # static linking
-LDFLGS=	-g -rdynamic
 
 # 
 # the subdirectory used by cfront compilers gets cleaned
@@ -112,10 +105,10 @@
 # general compilation rules for .cpp, .cxx, .c  files
 #
 .cpp.o:		
-	$(CXX) $(CFLGS) $(OPT) $(INC) -c $<
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $<
            
 .c.o:	   
-	$(CXX) $(CFLGS) $(OPT) $(INC) -c $<
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $<
 
 #
 # targets file included in generated makefile
@@ -593,17 +586,23 @@
    writeToRewriteReferenceFile.o \
    xsynchronize.o
 
+SUBDIRS := misc/454 misc/mktrace misc/phd2fasta
+
+all: consed $(SUBDIRS)
+
+$(SUBDIRS):
+	$(MAKE) -C $@
+
+.PHONY: all $(SUBDIRS)
+
 consed:	$(CONSED_OBJS) makefile checkLicenseKeyStub.o
-	$(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \
-		$(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS)
 
 trial_consed: 	$(CONSED_OBJS) makefile checkLicenseKey.o
-	$(CXX) $(INC) $(LDFLGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o \
-		$(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o $(ALL_LIBS)
 
 pure:	$(CONSED_OBJS) makefile checkLicenseKeyStub.o
-	$(PURIFY) $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \
-		$(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS)
+	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS)
 
 clean:	
 	rm -rf *.o core $(TEMPLATE_DIR)
@@ -613,15 +612,15 @@
 # the Solaris 5.x compiler cannot optimize the following
 
 consedResources.o:
-	$(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources.cpp
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources.cpp
 
 consedResources2.o:
-	$(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources2.cpp
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources2.cpp
 
 # tlingit cannot optimize the following:
 
 guiEditResources.o:
-	$(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c guiEditResources.cpp
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c guiEditResources.cpp
 
 guiEditResources.o : \
 	 assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \
--- a/misc/454/Makefile
+++ b/misc/454/Makefile
@@ -0,0 +1,16 @@
+CC ?= cc
+LIBM = -lm
+
+DEFS = -DANSI_C
+
+OBJS= sff2scf.c
+
+sff2scf: $(OBJS)
+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
+
+.c.o:	   
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
+
+clean:
+	rm -f $(OBJS) sff2scf
+
--- a/misc/mktrace/Makefile
+++ b/misc/mktrace/Makefile
@@ -1,13 +1,17 @@
-CC= cc
-CFLAGS= -g
-CLIB= -lm
+CC ?= cc
+LIBM = -lm
+
+DEFS = -DANSI_C
 
 OBJS= mktrace.o readFASTA.o writeSCF.o synTrace.o \
       freeTrace.o rwUtil.o writePhd.o getTime.o \
       readQUAL.o
 
 mktrace: $(OBJS)
-	$(CC) $(CFLAGS) -o mktrace $(OBJS) $(CLIB)
+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
+
+.c.o:	   
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
 
 clean:
 	rm -f $(OBJS) mktrace
--- a/misc/phd2fasta/Makefile
+++ b/misc/phd2fasta/Makefile
@@ -1,8 +1,9 @@
-CC=cc
-CFLAGS=-O -w
-CLIB=-lm
+CC ?= cc
+LIBM = -lm
 
-OBJ= phd2fasta.o \
+DEFS = -DANSI_C
+
+OBJS= phd2fasta.o \
      readParam.o initParam.o checkParam.o \
      freeParam.o helpParam.o \
      readFOF.o readDIR.o readFOX.o \
@@ -15,10 +16,11 @@
 
 INC= phd2fasta.h
 
-SRC = $(OBJ:.o=.c)
-
-phd2fasta: $(OBJ)
-	$(CC) $(CFLAGS) -o phd2fasta $(OBJ) $(CLIB)
+phd2fasta: $(OBJS)
+	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM)
+           
+.c.o:	   
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $<
 
 clean:
 	rm -f $(OBJ) phd2fasta