add popt and new command line and config dir code.

src/zmapUtils/makefile

@@ -13,9 +13,11 @@ MAKE_DIR = $(ROOT_DIRECTORY)/zmapMake
 # local macros
 UTILS_PRIV_HDRS = zmapReadLine_P.h zmapUtils_P.h 
 PUB_HDRS = zmapReadLine.h zmapSys.h zmapUtils.h zmapUtilsCheck.h zmapUtilsDebug.h zmapUtilsLog.h zmapUtilsMesg.h
-UTILS_SRC = zmapUtils.c zmapGUIutils.c zmapLogging.c zmapFileUtils.c zmapReadLine.c zmapUtilsConfig.c
-UTILS_OBJ = zmapUtils.o zmapGUIutils.o zmapLogging.o zmapFileUtils.o zmapReadLine.o zmapUtilsConfig.o
-
+UTILS_SRC = zmapUtils.c zmapGUIutils.c zmapLogging.c zmapFileUtils.c \
+            zmapReadLine.c zmapUtilsConfig.c zmapCmdLineArgs.c zmapConfigDir.c
+UTILS_OBJ = zmapUtils.o zmapGUIutils.o zmapLogging.o zmapFileUtils.o \
+            zmapReadLine.o zmapUtilsConfig.o zmapCmdLineArgs.o zmapConfigDir.o
+CURRENT_INC = -I/nfs/team71/acedb/edgrif/ZMap/popt/popt-ins/include
 
 #
 # These must all be set for the common includes to work.