Make in-place repair an option to bot manifold

This is for automatically repairing all bots in a file or hierarchy at
once via search exec in MGED:

search -type bot ! -type plate -exec "bot manifold -i {}" ";"

The above line will check all the non plate mode bots to see if they are
manifold.  If not, repair will be attempted to update the BoT to be
manifold via either small adjustments by the Manifold library or (if
that fails, which is more typical) hole filling using geogram.

src/libged/bot/manifold.cpp

@@ -263,7 +263,15 @@ geogram_mesh_repair(struct rt_bot_internal *bot)
 }
 #endif
 
-//#define IN_PLACE_REPAIR
+static void
+manifold_usage(struct bu_vls *str, const char *cmd, struct bu_opt_desc *d) {
+    char *option_help = bu_opt_describe(d, NULL);
+    bu_vls_sprintf(str, "Usage: %s [options] input_bot [output_name]\n", cmd);
+    if (option_help) {
+	bu_vls_printf(str, "Options:\n%s\n", option_help);
+	bu_free(option_help, "help str");
+    }
+}
 
 extern "C" int
 _bot_cmd_manifold(void *bs, int argc, const char **argv)
@@ -276,13 +284,31 @@ _bot_cmd_manifold(void *bs, int argc, const char **argv)
 
     struct _ged_bot_info *gb = (struct _ged_bot_info *)bs;
 
+    // We know we're the manifold command - start processing args
     argc--; argv++;
 
-#ifdef IN_PLACE_REPAIR
-    if (argc != 1) {
-#else
-    if (argc != 1 && argc != 2) {
-#endif
+    int print_help = 0;
+    int in_place_repair = 0;
+
+    struct bu_opt_desc d[5];
+    BU_OPT(d[0], "h",      "help",     "",            NULL, &print_help,      "Print help");
+    BU_OPT(d[1], "i",  "in-place",     "",            NULL, &in_place_repair, "Alter BoTs (if necessary) in place");
+    BU_OPT_NULL(d[2]);
+
+    int ac = bu_opt_parse(NULL, argc, argv, d);
+    argc = ac;
+
+    if (print_help || !argc) {
+	manifold_usage(gb->gedp->ged_result_str, "bot manifold", d);
+	return GED_HELP;
+    }
+
+    if (in_place_repair && argc != 1) {
+	bu_vls_printf(gb->gedp->ged_result_str, "%s", usage_string);
+	return BRLCAD_ERROR;
+    }
+
+    if (!in_place_repair && argc != 1 && argc != 2) {
 	bu_vls_printf(gb->gedp->ged_result_str, "%s", usage_string);
 	return BRLCAD_ERROR;
     }
@@ -297,11 +323,7 @@ _bot_cmd_manifold(void *bs, int argc, const char **argv)
 	return BRLCAD_ERROR;
     }
 
-#ifdef IN_PLACE_REPAIR
-    int repair_flag = 1;
-#else
-    int repair_flag = (argc == 2) ?  1 : 0;
-#endif
+    int repair_flag = (in_place_repair || argc == 2) ?  1 : 0;
 
     struct rt_bot_internal *mbot = manifold_process(bot, repair_flag);
 
@@ -326,18 +348,19 @@ _bot_cmd_manifold(void *bs, int argc, const char **argv)
 	intern.idb_meth = &OBJ[ID_BOT];
 	intern.idb_ptr = (void *)mbot;
 
-#ifdef IN_PLACE_REPAIR
-	const char *rname = gb->dp->d_namep;
-	struct directory *dp = gb->dp;
-#else
-	const char *rname = argv[1];
-
-	struct directory *dp = db_diradd(gb->gedp->dbip, rname, RT_DIR_PHONY_ADDR, 0, RT_DIR_SOLID, (void *)&intern.idb_type);
-	if (dp == RT_DIR_NULL) {
-	    bu_vls_printf(gb->gedp->ged_result_str, "Failed to write out new BoT %s", rname);
-	    return BRLCAD_ERROR;
+	const char *rname;
+	struct directory *dp;
+	if (in_place_repair) {
+	    rname = gb->dp->d_namep;
+	    dp = gb->dp;
+	} else {
+	    rname = argv[1];
+	    dp = db_diradd(gb->gedp->dbip, rname, RT_DIR_PHONY_ADDR, 0, RT_DIR_SOLID, (void *)&intern.idb_type);
+	    if (dp == RT_DIR_NULL) {
+		bu_vls_printf(gb->gedp->ged_result_str, "Failed to write out new BoT %s", rname);
+		return BRLCAD_ERROR;
+	    }
 	}
-#endif
 
 	if (rt_db_put_internal(dp, gb->gedp->dbip, &intern, &rt_uniresource) < 0) {
 	    bu_vls_printf(gb->gedp->ged_result_str, "Failed to write out new BoT %s", rname);
@@ -366,18 +389,19 @@ _bot_cmd_manifold(void *bs, int argc, const char **argv)
     intern.idb_meth = &OBJ[ID_BOT];
     intern.idb_ptr = (void *)mbot;
 
-
-#ifdef IN_PLACE_REPAIR
-    const char *rname = gb->dp->d_namep;
-    struct directory *dp = gb->dp;
-#else
-    const char *rname = argv[1];
-    struct directory *dp = db_diradd(gb->gedp->dbip, rname, RT_DIR_PHONY_ADDR, 0, RT_DIR_SOLID, (void *)&intern.idb_type);
-    if (dp == RT_DIR_NULL) {
-	bu_vls_printf(gb->gedp->ged_result_str, "Failed to write out new BoT %s", rname);
-	return BRLCAD_ERROR;
+    const char *rname;
+    struct directory *dp;
+    if (in_place_repair) {
+	rname = gb->dp->d_namep;
+	dp = gb->dp;
+    } else {
+	rname = argv[1];
+	dp = db_diradd(gb->gedp->dbip, rname, RT_DIR_PHONY_ADDR, 0, RT_DIR_SOLID, (void *)&intern.idb_type);
+	if (dp == RT_DIR_NULL) {
+	    bu_vls_printf(gb->gedp->ged_result_str, "Failed to write out new BoT %s", rname);
+	    return BRLCAD_ERROR;
+	}
     }
-#endif
 
     if (rt_db_put_internal(dp, gb->gedp->dbip, &intern, &rt_uniresource) < 0) {
 	bu_vls_printf(gb->gedp->ged_result_str, "Failed to write out new BoT %s", rname);