diff --git a/libsemanage/include/semanage/handle.h b/libsemanage/include/semanage/handle.h
index e303713..c746930 100644
--- a/libsemanage/include/semanage/handle.h
+++ b/libsemanage/include/semanage/handle.h
@@ -129,6 +129,12 @@ int semanage_mls_enabled(semanage_handle_t *sh);
 /* Change to alternate selinux root path */
 int semanage_set_root(const char *path);
 
+/* Get whether or not needless unused branch of tunables would be preserved */
+int semanage_get_preserve_tunables(semanage_handle_t * handle);
+
+/* Set whether or not to preserve the needless unused branch of tunables */
+void semanage_set_preserve_tunables(semanage_handle_t * handle, int preserve_tunables);
+
 /* META NOTES
  *
  * For all functions a non-negative number indicates success. For some
diff --git a/libsemanage/src/direct_api.c b/libsemanage/src/direct_api.c
index aac1974..8fcfb88 100644
--- a/libsemanage/src/direct_api.c
+++ b/libsemanage/src/direct_api.c
@@ -353,17 +353,11 @@ static int parse_module_headers(semanage_handle_t * sh, char *module_data,
 	     semanage_path(SEMANAGE_TMP, SEMANAGE_MODULES)) == NULL) {
 		return -1;
 	}
-	if (asprintf(filename, "%s/%s.pp%s", module_path, *module_name, DISABLESTR) == -1) {
+	if (asprintf(filename, "%s/%s.pp", module_path, *module_name) == -1) {
 		ERR(sh, "Out of memory!");
 		return -1;
 	}
 
-	if (access(*filename, F_OK) == -1) {
-		char *ptr = *filename;
-		int len = strlen(ptr) - strlen(DISABLESTR);
-		if (len > 0) ptr[len]='\0';
-	}
-
 	return 0;
 }
 
@@ -695,7 +689,8 @@ static int semanage_direct_commit(semanage_handle_t * sh)
 
 	/* Declare some variables */
 	int modified = 0, fcontexts_modified, ports_modified,
-	    seusers_modified, users_extra_modified, dontaudit_modified;
+	    seusers_modified, users_extra_modified, dontaudit_modified,
+	    preserve_tunables_modified;
 	dbase_config_t *users = semanage_user_dbase_local(sh);
 	dbase_config_t *users_base = semanage_user_base_dbase_local(sh);
 	dbase_config_t *pusers_base = semanage_user_base_dbase_policy(sh);
@@ -737,6 +732,31 @@ static int semanage_direct_commit(semanage_handle_t * sh)
 		}
 	}
 
+	/* Create or remove the preserve_tunables flag file. */
+	path = semanage_path(SEMANAGE_TMP, SEMANAGE_PRESERVE_TUNABLES);
+	if (access(path, F_OK) == 0)
+		preserve_tunables_modified = !(sepol_get_preserve_tunables(sh->sepolh) == 1);
+	else
+		preserve_tunables_modified = (sepol_get_preserve_tunables(sh->sepolh) == 1);
+	if (sepol_get_preserve_tunables(sh->sepolh) == 1) {
+		FILE *touch;
+		touch = fopen(path, "w");
+		if (touch != NULL) {
+			if (fclose(touch) != 0) {
+				ERR(sh, "Error attempting to create preserve_tunable flag.");
+				goto cleanup;
+			}
+		} else {
+			ERR(sh, "Error attempting to create preserve_tunable flag.");
+			goto cleanup;
+		}
+	} else {
+		if (remove(path) == -1 && errno != ENOENT) {
+			ERR(sh, "Error removing the preserve_tunables flag.");
+			goto cleanup;
+		}
+	}
+
 	/* Before we do anything else, flush the join to its component parts.
 	 * This *does not* flush to disk automatically */
 	if (users->dtable->is_modified(users->dbase)) {
@@ -759,6 +779,7 @@ static int semanage_direct_commit(semanage_handle_t * sh)
 	modified |= ifaces->dtable->is_modified(ifaces->dbase);
 	modified |= nodes->dtable->is_modified(nodes->dbase);
 	modified |= dontaudit_modified;
+	modified |= preserve_tunables_modified;
 
 	/* If there were policy changes, or explicitly requested, rebuild the policy */
 	if (sh->do_rebuild || modified) {
@@ -1307,29 +1328,12 @@ static int semanage_direct_enable(semanage_handle_t * sh, char *module_name)
 		base++;
 		if (memcmp(module_name, base, name_len) == 0) {
 
-			if(strcmp(base + name_len + 3, DISABLESTR) != 0) {
-				ERR(sh, "Module %s is already enabled.", module_name);
+			if (semanage_enable_module(module_filenames[i]) < 0) {
+				ERR(sh, "Could not enable module %s.", module_name);
 				retval = -2;
 				goto cleanup;
 			}
-
-			int len = strlen(module_filenames[i]) - strlen(DISABLESTR);
-			char *enabled_name = calloc(1, len+1);
-			if (!enabled_name) {
-				ERR(sh, "Could not allocate memory");
-				retval = -1;
-				goto cleanup;
-			}
-
-			strncpy(enabled_name, module_filenames[i],len);
-
-			if (rename(module_filenames[i], enabled_name) == -1) {
-				ERR(sh, "Could not enable module file %s.",
-				    enabled_name);
-				retval = -2;
-			}
 			retval = 0;
-			free(enabled_name);
 			goto cleanup;
 		}
 	}
@@ -1363,28 +1367,14 @@ static int semanage_direct_disable(semanage_handle_t * sh, char *module_name)
 			goto cleanup;
 		}
 		base++;
-		if (memcmp(module_name, base, name_len) == 0) {
-			if (strcmp(base + name_len + 3, DISABLESTR) == 0) {
-				ERR(sh, "Module %s is already disabled.", module_name);
+		if ((memcmp(module_name, base, name_len) == 0) &&
+		    (strcmp(base + name_len, ".pp") == 0)) {
+			if (semanage_disable_module(module_filenames[i]) < 0) {
 				retval = -2;
 				goto cleanup;
-			} else if (strcmp(base + name_len, ".pp") == 0) {
-				char disabled_name[PATH_MAX];
-				if (snprintf(disabled_name, PATH_MAX, "%s%s", 
-							module_filenames[i], DISABLESTR) == PATH_MAX) {
-					ERR(sh, "Could not disable module file %s.",
-							module_filenames[i]);
-					retval = -2;
-					goto cleanup;
-				}
-				if (rename(module_filenames[i], disabled_name) == -1) {
-					ERR(sh, "Could not disable module file %s.",
-							module_filenames[i]);
-					retval = -2;
-				}
-				retval = 0;
-				goto cleanup;
 			}
+			retval=0;
+			goto cleanup;
 		}
 	}
 	ERR(sh, "Module %s was not found.", module_name);
@@ -1418,6 +1408,7 @@ static int semanage_direct_remove(semanage_handle_t * sh, char *module_name)
 		}
 		base++;
 		if (memcmp(module_name, base, name_len) == 0) {
+			semanage_enable_module(module_filenames[i]);
 			if (unlink(module_filenames[i]) == -1) {
 				ERR(sh, "Could not remove module file %s.",
 				    module_filenames[i]);
diff --git a/libsemanage/src/genhomedircon.c b/libsemanage/src/genhomedircon.c
index 847d87e..2870fa8 100644
--- a/libsemanage/src/genhomedircon.c
+++ b/libsemanage/src/genhomedircon.c
@@ -314,6 +314,8 @@ static semanage_list_t *get_home_dirs(genhomedircon_settings_t * s)
 		}
 		if (strcmp(pwbuf->pw_dir, "/") == 0)
 			continue;
+		if (strcmp(pwbuf->pw_dir, "/root") == 0)
+			continue;
 		if (semanage_str_count(pwbuf->pw_dir, '/') <= 1)
 			continue;
 		if (!(path = strdup(pwbuf->pw_dir))) {
@@ -829,6 +831,8 @@ static genhomedircon_user_entry_t *get_users(genhomedircon_settings_t * s,
 			 * /root */
 			continue;
 		}
+		if (strcmp(pwent->pw_dir, "/root") == 0)
+			continue;
 		if (push_user_entry(&head, name, seuname,
 				    prefix, pwent->pw_dir, level) != STATUS_SUCCESS) {
 			*errors = STATUS_ERR;
diff --git a/libsemanage/src/handle.c b/libsemanage/src/handle.c
index 647f0ee..7adc1cc 100644
--- a/libsemanage/src/handle.c
+++ b/libsemanage/src/handle.c
@@ -261,6 +261,19 @@ void semanage_set_disable_dontaudit(semanage_handle_t * sh, int disable_dontaudi
 	return;
 }
 
+int semanage_get_preserve_tunables(semanage_handle_t * sh)
+{
+	assert(sh != NULL);
+	return sepol_get_preserve_tunables(sh->sepolh);
+}
+
+void semanage_set_preserve_tunables(semanage_handle_t * sh,
+				    int preserve_tunables)
+{
+	assert(sh != NULL);
+	sepol_set_preserve_tunables(sh->sepolh, preserve_tunables);
+}
+
 void semanage_set_check_contexts(semanage_handle_t * sh, int do_check_contexts)
 {
 
diff --git a/libsemanage/src/libsemanage.map b/libsemanage/src/libsemanage.map
index 3222e3d..2827abe 100644
--- a/libsemanage/src/libsemanage.map
+++ b/libsemanage/src/libsemanage.map
@@ -22,5 +22,6 @@ LIBSEMANAGE_1.0 {
 	  semanage_is_connected; semanage_get_disable_dontaudit; semanage_set_disable_dontaudit;
 	  semanage_mls_enabled;
 	  semanage_set_check_contexts;
+	  semanage_get_preserve_tunables; semanage_set_preserve_tunables;
   local: *;
 };
diff --git a/libsemanage/src/semanage_store.c b/libsemanage/src/semanage_store.c
index 8d6ff1c..e322992 100644
--- a/libsemanage/src/semanage_store.c
+++ b/libsemanage/src/semanage_store.c
@@ -57,7 +57,7 @@ typedef struct dbase_policydb dbase_t;
 
 #include "debug.h"
 
-const char *DISABLESTR=".disabled";
+static const char *DISABLESTR="disabled";
 
 #define SEMANAGE_CONF_FILE "semanage.conf"
 /* relative path names to enum semanage_paths to special files and
@@ -117,6 +117,7 @@ static const char *semanage_sandbox_paths[SEMANAGE_STORE_NUM_PATHS] = {
 	"/netfilter_contexts",
 	"/file_contexts.homedirs",
 	"/disable_dontaudit",
+	"/preserve_tunables",
 };
 
 /* A node used in a linked list of file contexts; used for sorting.
@@ -425,6 +426,13 @@ int semanage_store_access_check(void)
 
 /********************* other I/O functions *********************/
 
+static int is_disabled_file(const char *file) {
+	char *ptr = strrchr(file, '.');
+	if (! ptr) return 0;
+	ptr++;
+	return (strcmp(ptr, DISABLESTR) == 0);
+}
+
 /* Callback used by scandir() to select files. */
 static int semanage_filename_select(const struct dirent *d)
 {
@@ -435,11 +443,41 @@ static int semanage_filename_select(const struct dirent *d)
 	return 1;
 }
 
+int semanage_disable_module(const char *file) {
+	char path[PATH_MAX];
+	int in;
+	int n = snprintf(path, PATH_MAX, "%s.%s", file, DISABLESTR);
+	if (n < 0 || n >= PATH_MAX)
+		return -1;
+	if ((in = open(path, O_WRONLY | O_CREAT, S_IRUSR | S_IWUSR)) == -1) {
+		return -1;
+	}
+	close(in);
+	return 0;
+}
+
+int semanage_enable_module(const char *file) {
+	char path[PATH_MAX];
+	int n = snprintf(path, PATH_MAX, "%s.%s", file, DISABLESTR);
+	if (n < 0 || n >= PATH_MAX)
+		return 1;
+
+	if ((unlink(path) < 0) && (errno != ENOENT))
+		return -1;
+	return 0;
+}
+
 int semanage_module_enabled(const char *file) {
-	int len = strlen(file) - strlen(DISABLESTR);
-	return (len < 0 || strcmp(&file[len], DISABLESTR) != 0);
+	char path[PATH_MAX];
+	if (is_disabled_file(file)) return 0;
+	int n = snprintf(path, PATH_MAX, "%s.%s", file, DISABLESTR);
+	if (n < 0 || n >= PATH_MAX)
+		return 1;
+
+	return (access(path, F_OK ) != 0);
 }
 
+/* Callback used by scandir() to select module files. */
 static int semanage_modulename_select(const struct dirent *d)
 {
 	if (d->d_name[0] == '.'
@@ -447,7 +485,7 @@ static int semanage_modulename_select(const struct dirent *d)
 		|| (d->d_name[1] == '.' && d->d_name[2] == '\0')))
 		return 0;
 
-	return semanage_module_enabled(d->d_name);
+	return (! is_disabled_file(d->d_name));
 }
 
 /* Copies a file from src to dst.  If dst already exists then
@@ -684,7 +722,7 @@ int semanage_get_modules_names(semanage_handle_t * sh, char ***filenames,
 			       int *len)
 {
 	return semanage_get_modules_names_filter(sh, filenames,
-						 len, semanage_filename_select);
+						 len, semanage_modulename_select);
 }
 
 /* Scans the modules directory for the current semanage handler.  This
@@ -697,8 +735,25 @@ int semanage_get_modules_names(semanage_handle_t * sh, char ***filenames,
 int semanage_get_active_modules_names(semanage_handle_t * sh, char ***filenames,
 			       int *len)
 {
-	return semanage_get_modules_names_filter(sh, filenames,
-						 len, semanage_modulename_select);
+
+	int rc = semanage_get_modules_names_filter(sh, filenames,
+						   len, semanage_modulename_select);
+	if ( rc != 0 ) return rc;
+
+	int i = 0, num_modules = *len;
+	char **names=*filenames;
+
+	while ( i < num_modules ) {
+		if (! semanage_module_enabled(names[i])) {
+			free(names[i]);
+			names[i]=names[num_modules-1];
+			names[num_modules-1] = NULL;
+			num_modules--;
+		}
+		i++;
+	}
+	*len = num_modules;
+	return 0;
 }
 
 /******************* routines that run external programs *******************/
diff --git a/libsemanage/src/semanage_store.h b/libsemanage/src/semanage_store.h
index a0b2dd8..b451308 100644
--- a/libsemanage/src/semanage_store.h
+++ b/libsemanage/src/semanage_store.h
@@ -59,6 +59,7 @@ enum semanage_sandbox_defs {
 	SEMANAGE_NC,
 	SEMANAGE_FC_HOMEDIRS,
 	SEMANAGE_DISABLE_DONTAUDIT,
+	SEMANAGE_PRESERVE_TUNABLES,
 	SEMANAGE_STORE_NUM_PATHS
 };
 
@@ -85,6 +86,8 @@ int semanage_get_modules_names(semanage_handle_t * sh,
 			       char ***filenames, int *len);
 
 int semanage_module_enabled(const char *file);
+int semanage_enable_module(const char *file);
+int semanage_disable_module(const char *file);
 /* lock file routines */
 int semanage_get_trans_lock(semanage_handle_t * sh);
 int semanage_get_active_lock(semanage_handle_t * sh);
@@ -129,6 +132,4 @@ int semanage_nc_sort(semanage_handle_t * sh,
 		     size_t buf_len,
 		     char **sorted_buf, size_t * sorted_buf_len);
 
-extern const char *DISABLESTR;
-
 #endif