diff --git a/libsemanage/src/Makefile b/libsemanage/src/Makefile
index d21e972..d9120c0 100644
--- a/libsemanage/src/Makefile
+++ b/libsemanage/src/Makefile
@@ -10,7 +10,8 @@ LIBDIR ?= $(PREFIX)/lib
 SHLIBDIR ?= $(PREFIX)/lib
 INCLUDEDIR ?= $(PREFIX)/include
 PYLIBVER ?= $(shell $(PYTHON) -c 'import sys;print("python%d.%d" % sys.version_info[0:2])')
-PYINC ?= $(shell pkg-config --cflags `basename $(PYTHON)`)
+PYINC ?= $(shell pkg-config --cflags $(PYPREFIX))
+PYTHONLIBDIR ?= $(shell pkg-config --libs $(PYPREFIX))
 PYLIBDIR ?= $(LIBDIR)/$(PYLIBVER)
 RUBYLIBVER ?= $(shell ruby -e 'print RUBY_VERSION.split(".")[0..1].join(".")')
 RUBYPLATFORM ?= $(shell ruby -e 'print RUBY_PLATFORM')
@@ -76,7 +77,7 @@ $(SWIGRUBYLOBJ): $(SWIGRUBYCOUT)
 	$(CC) $(filter-out -Werror, $(CFLAGS)) -I$(RUBYINC) -fPIC -DSHARED -c -o $@ $<
 
 $(SWIGSO): $(SWIGLOBJ)
-	$(CC) $(CFLAGS) $(LDFLAGS) -shared -o $@ $< -L. -lsemanage -L$(LIBDIR) -Wl,-soname,$@,-z,defs
+	$(CC) $(CFLAGS) $(LDFLAGS) -shared -o $@ $< -L. -lsemanage -L$(LIBDIR) $(PYTHONLIBDIR) -Wl,-soname,$@,-z,defs
 
 $(SWIGRUBYSO): $(SWIGRUBYLOBJ)
 	$(CC) $(CFLAGS) $(LDFLAGS) -shared -o $@ $^ -L. -lsemanage -L$(LIBDIR) -Wl,-soname,$@
diff --git a/libsemanage/src/direct_api.c b/libsemanage/src/direct_api.c
index aac1974..3dfa279 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;
 }
 
@@ -1307,29 +1301,12 @@ 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 +1340,14 @@ 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 +1381,7 @@ 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/semanage_store.c b/libsemanage/src/semanage_store.c
index 8d6ff1c..37b0c7a 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
@@ -425,6 +425,13 @@ 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 +442,41 @@ 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 +484,7 @@ 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 +721,7 @@ 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 +734,25 @@ 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..e980cdc 100644
--- a/libsemanage/src/semanage_store.h
+++ b/libsemanage/src/semanage_store.h
@@ -85,6 +85,8 @@ 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 +131,4 @@ 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