diff -r -u GMT4.1.1.old/Makefile GMT4.1.1/Makefile
--- GMT4.1.1.old/Makefile	2006-02-27 19:25:01.000000000 -0500
+++ GMT4.1.1/Makefile	2006-03-03 16:55:56.000000000 -0500
@@ -109,19 +109,21 @@
 		done
 
 mex_config:	
+		if [ -d src/mex ]; then \
 		if [ ! -f src/mex/makefile ]; then \
 			cd src/mex; \
 			\rm -f config.{cache,log,status}; \
 			./configure; \
+		fi \
 		fi
-		
 xgrid_config:	
+		if [ -d src/xgrid ]; then \
 		if [ ! -f src/xgrid/makefile ]; then \
 			cd src/xgrid; \
 			\rm -f config.{cache,log,status}; \
 			./configure; \
+		fi \
 		fi
-
 gmtmacros:	
 		if [ ! -s src/makegmt.macros ]; then \
 			echo "src/makegmt.macros is empty - you must rerun configure in the main GMT directory"; \
diff -r -u GMT4.1.1.old/src/gmt_init.c GMT4.1.1/src/gmt_init.c
--- GMT4.1.1.old/src/gmt_init.c	2006-02-22 17:52:55.000000000 -0500
+++ GMT4.1.1/src/gmt_init.c	2006-03-03 15:23:01.000000000 -0500
@@ -2351,7 +2351,7 @@
 
 	if (get == 0) {	/* Must use GMT system defaults via gmt.conf */
 
-		sprintf (line, "%s%cshare%cgmt.conf", GMTHOME, DIR_DELIM, DIR_DELIM);
+	        sprintf (line, "%s%cshare%cgmt%cgmt.conf", GMTHOME, DIR_DELIM, DIR_DELIM,DIR_DELIM);
 		if ((fp = fopen (line, "r")) == NULL) {
 			fprintf (stderr, "GMT Fatal Error: Cannot open/find GMT configuration file %s\n", line);
 			exit (EXIT_FAILURE);
@@ -2372,7 +2372,7 @@
 		id = get;
 
 	id--;	/* Get 0 or 1 */
-	sprintf (line, "%s%cshare%c.gmtdefaults_%s", GMTHOME, DIR_DELIM, DIR_DELIM, suffix[id]);
+	sprintf (line, "%s%cshare%cgmt%c.gmtdefaults_%s", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, suffix[id]);
 
 	path = (char *) GMT_memory (VNULL, (size_t)(strlen (line) + 1), (size_t)1, GMT_program);
 
@@ -2481,7 +2481,7 @@
 		FILE *fp;
 		char line[BUFSIZ], path[BUFSIZ];
 
-		sprintf (path, "%s%cshare%c%s", GMTHOME, DIR_DELIM, DIR_DELIM, name);
+		sprintf (path, "%s%cshare%cgmt%c%s", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, name);
 
 		if (!strcmp ("Sphere", name)) {
 			/* Special case where previous setting in .gmtdefaults4 is a custom ellipse which
@@ -2560,7 +2560,7 @@
 
 	GMT_set_home ();
 
-	sprintf (line, "%s%cshare%cgmtmedia.d", GMTHOME, DIR_DELIM, DIR_DELIM);
+	sprintf (line, "%s%cshare%cgmt%gmtmedia.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 	if ((fp = fopen (line, "r")) == NULL) return (0);
 
 	n_alloc = GMT_TINY_CHUNK;
@@ -2618,10 +2618,10 @@
 	char file[BUFSIZ], line[BUFSIZ], full[16], abbrev[16], c[16], dwu;
 	int i, nm = 0, nw = 0, nu = 0;
 
-	sprintf (file, "%s%cshare%ctime%c%s.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, name);
+	sprintf (file, "%s%cshare%cgmt%ctime%c%s.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM, name);
 	if ((fp = fopen (file, "r")) == NULL) {
 		fprintf (stderr, "GMT Warning: Could not load %s - revert to us (English)!\n", name);
-		sprintf (file, "%s%cshare%ctime%cus.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
+		sprintf (file, "%s%cshare%cgmt%ctime%cus.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 		if ((fp = fopen (file, "r")) == NULL) {
 			fprintf (stderr, "GMT Error: Could not find %s!\n", file);
 			exit (EXIT_FAILURE);
@@ -4809,7 +4809,7 @@
 	int code = 0, pos;
 	FILE *in;
 
-	sprintf (line, "%s%cshare%cpslib%c%s.ps", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, enc->name);
+	sprintf (line, "%s%cshare%cgmt%cpslib%c%s.ps", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM, enc->name);
 	in = GMT_fopen (line, "r");
 
 	if (!in)
@@ -4886,7 +4886,7 @@
 
 	/* First the standard 35 PostScript fonts from Adobe */
 
-	sprintf (fullname, "%s%cshare%cpslib%cPS_font_info.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
+	sprintf (fullname, "%s%cshare%cgmt%cpslib%cPS_font_info.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 
 	if ((in = fopen (fullname, "r")) == NULL)
 	{
@@ -4916,7 +4916,7 @@
 
  	/* Then any custom fonts */
 
-	sprintf (fullname, "%s%cshare%cpslib%cCUSTOM_font_info.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
+	sprintf (fullname, "%s%cshare%cgmt%cpslib%cCUSTOM_font_info.d", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 
 	if (!access (fullname, R_OK)) {	/* Decode Custom font file */
 
diff -r -u GMT4.1.1.old/src/gmt_support.c GMT4.1.1/src/gmt_support.c
--- GMT4.1.1.old/src/gmt_support.c	2006-02-20 20:51:21.000000000 -0500
+++ GMT4.1.1/src/gmt_support.c	2006-03-03 15:28:29.000000000 -0500
@@ -1009,9 +1009,9 @@
 
 	if (!ok) {	/* No table in current dir, try /share */
 		if (table)
-			sprintf (CPT_file, "%s%cshare%ccpt%cGMT_%s.cpt", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, table);
+		  sprintf (CPT_file, "%s%cshare%cgmt%ccpt%cGMT_%s.cpt", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM, table);
 		else	/* Default to rainbow colors */
-			sprintf (CPT_file, "%s%cshare%ccpt%cGMT_rainbow.cpt", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
+		  sprintf (CPT_file, "%s%cshare%cgmt%ccpt%cGMT_rainbow.cpt", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 
 		ok = !access (CPT_file, R_OK);
 		if (!ok)
@@ -5457,7 +5457,7 @@
 
 	/* First check the $GMTHOME/share directory */
 
-	sprintf (path, "%s%cshare%c%s", GMTHOME, DIR_DELIM, DIR_DELIM, name);
+	sprintf (path, "%s%cshare%cgmt%c%s", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, name);
 	if (!access (path, R_OK)) return (TRUE);	/* File exists and is readable, return with name */
 
 	/* File was not readable.  Now check if it exists */
@@ -5471,7 +5471,7 @@
 	 * It is not an error if we cannot find the named file, only if it is found
 	 * but cannot be read due to permission problems */
 
-	sprintf (dir, "%s%cshare%ccoastline.conf", GMTHOME, DIR_DELIM, DIR_DELIM);
+	sprintf (dir, "%s%cshare%cgmt%ccoastline.conf", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 	if (!access (dir, F_OK))  { /* File exists... */
 		if (access (dir, R_OK)) {	/* ...but cannot be read */
 			fprintf (stderr, "%s: Error: GMT does not have permission to open %s!\n", GMT_program, dir);
@@ -6100,7 +6100,7 @@
 
 	/* Open the list in $GMTHOME/share */
 
-	sprintf (list, "%s%cshare%cGMT_CustomSymbols.lis", GMTHOME, DIR_DELIM, DIR_DELIM);
+	sprintf (list, "%s%cshare%cgmt%cGMT_CustomSymbols.lis", GMTHOME, DIR_DELIM, DIR_DELIM);
 
 	if ((fp = fopen (list, "r")) == NULL) {
 		fprintf (stderr, "%s: ERROR: Cannot open file %s\n", GMT_program, list);
@@ -7876,7 +7876,7 @@
 	sprintf (file, "%s.def", name);
 
 	if (access (file, R_OK)) {	/* Not in current dir, try GMTHOME */
-		sprintf (file, "%s%cshare%ccustom%c%s.def", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, name);
+	  sprintf (file, "%s%cshare%cgmt%ccustom%c%s.def", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM, name);
 		if (access (file, R_OK)) {	/* Not there either - give up */
 			fprintf (stderr, "GMT ERROR: %s : Could not find custom symbol %s\n", GMT_program, name);
 			exit (EXIT_FAILURE);
diff -r -u GMT4.1.1.old/src/grd2cpt.c GMT4.1.1/src/grd2cpt.c
--- GMT4.1.1.old/src/grd2cpt.c	2005-12-17 00:59:22.000000000 -0500
+++ GMT4.1.1/src/grd2cpt.c	2006-03-03 15:29:44.000000000 -0500
@@ -70,7 +70,7 @@
 
 	/* Get list of available color tables in $GMTHOME/share/cpt */
 
-	sprintf (CPT_lis, "%s%cshare%cGMT_CPT.lis", GMTHOME, DIR_DELIM, DIR_DELIM);
+	sprintf (CPT_lis, "%s%cshare%cgmt%cGMT_CPT.lis", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 
 	if ((fpc = fopen (CPT_lis, "r")) == NULL) {
 		fprintf (stderr, "%s: ERROR: Cannot open file %s\n", GMT_program, CPT_lis);
diff -r -u GMT4.1.1.old/src/makecpt.c GMT4.1.1/src/makecpt.c
--- GMT4.1.1.old/src/makecpt.c	2005-12-17 00:59:22.000000000 -0500
+++ GMT4.1.1/src/makecpt.c	2006-03-03 15:30:22.000000000 -0500
@@ -48,7 +48,7 @@
 
 	/* Get list of available color tables in $GMTHOME/share/cpt */
 
-	sprintf (CPT_lis, "%s%cshare%cGMT_CPT.lis", GMTHOME, DIR_DELIM, DIR_DELIM);
+	sprintf (CPT_lis, "%s%cshare%cgmt%cGMT_CPT.lis", GMTHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 
 	if ((fpc = fopen (CPT_lis, "r")) == NULL) {
 		fprintf (stderr, "%s: ERROR: Cannot open file %s\n", GMT_program, CPT_lis);
diff -r -u GMT4.1.1.old/src/pslib.c GMT4.1.1/src/pslib.c
--- GMT4.1.1.old/src/pslib.c	2006-01-22 23:41:58.000000000 -0500
+++ GMT4.1.1/src/pslib.c	2006-03-03 15:32:34.000000000 -0500
@@ -889,7 +889,7 @@
 	if ((image_no >= 0 && image_no < N_PATTERNS) && ps_pattern[image_no].status) return (image_no);	/* Already done this */
 
 	if ((image_no >= 0 && image_no < N_PATTERNS))	/* Premade pattern yet not used */
-		sprintf (file, "%s%cshare%cpattern%cps_pattern_%2.2d.ras", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, image_no);
+	  sprintf (file, "%s%cshare%cgmt%cpattern%cps_pattern_%2.2d.ras", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM, image_no);
 	else {	/* User image, check to see if already used */
 
 		for (i = 0, found = FALSE; !found && i < ps_n_userimages; i++) found = !strcmp (ps_user_image[i], imagefile);
@@ -905,7 +905,7 @@
 			if (!access (imagefile, R_OK))
 				strcpy (file, imagefile);
 			else
-				sprintf (file, "%s%cshare%c%s", PSHOME, DIR_DELIM, DIR_DELIM, imagefile);
+			  sprintf (file, "%s%cshare%cgmt%c%s", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, imagefile);
 		}
 		ps_user_image[ps_n_userimages] = (char *) ps_memory (VNULL, (size_t)(strlen (imagefile)+1), sizeof (char));
 		strcpy (ps_user_image[ps_n_userimages], imagefile);
@@ -4187,7 +4187,7 @@
 	char buf[80];
 	char fullname[BUFSIZ];
 
-	sprintf (fullname, "%s%cshare%cpslib%c%s.ps", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, fname);
+	sprintf (fullname, "%s%cshare%cgmt%cpslib%c%s.ps", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM, fname);
 
 	in = fopen (fullname, "r");
 	if (in == NULL)
@@ -4212,7 +4212,7 @@
 
 	/* First the standard 35 PostScript fonts from Adobe */
 
-	sprintf (fullname, "%s%cshare%cpslib%cPS_font_info.d", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
+	sprintf (fullname, "%s%cshare%cgmt%cpslib%cPS_font_info.d", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 
 	if ((in = fopen (fullname, "r")) == NULL)
 	{
@@ -4242,7 +4242,7 @@
 
 	/* Then any custom fonts */
 
-	sprintf (fullname, "%s%cshare%cpslib%cCUSTOM_font_info.d", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM);
+	sprintf (fullname, "%s%cshare%cgmt%cpslib%cCUSTOM_font_info.d", PSHOME, DIR_DELIM, DIR_DELIM, DIR_DELIM, DIR_DELIM);
 
 	if (!access (fullname, R_OK)) {	/* Decode Custom font file */