Fix submodule leaks and invalid references

This cleans up some places I missed that could hold onto submodule
references and cleans up the way in which the repository cache is
both reloaded and released so that existing submodule references
aren't destroyed inappropriately.

src/checkout.c

@@ -328,12 +328,17 @@ static bool submodule_is_config_only(
 {
 	git_submodule *sm = NULL;
 	unsigned int sm_loc = 0;
+	bool rval = false;
 
-	if (git_submodule_lookup(&sm, data->repo, path) < 0 ||
-		git_submodule_location(&sm_loc, sm) < 0 ||
-		sm_loc == GIT_SUBMODULE_STATUS_IN_CONFIG)
+	if (git_submodule_lookup(&sm, data->repo, path) < 0)
 		return true;
 
+	if (git_submodule_location(&sm_loc, sm) < 0 ||
+		sm_loc == GIT_SUBMODULE_STATUS_IN_CONFIG)
+		rval = true;
+
+	git_submodule_free(sm);
+
 	return false;
 }
 
@@ -1262,7 +1267,6 @@ static int checkout_submodule(
 	const git_diff_file *file)
 {
 	int error = 0;
-	git_submodule *sm;
 
 	/* Until submodules are supported, UPDATE_ONLY means do nothing here */
 	if ((data->strategy & GIT_CHECKOUT_UPDATE_ONLY) != 0)
@@ -1273,7 +1277,7 @@ static int checkout_submodule(
 			data->opts.dir_mode, GIT_MKDIR_PATH)) < 0)
 		return error;
 
-	if ((error = git_submodule_lookup(&sm, data->repo, file->path)) < 0) {
+	if ((error = git_submodule_lookup(NULL, data->repo, file->path)) < 0) {
 		/* I've observed repos with submodules in the tree that do not
 		 * have a .gitmodules - core Git just makes an empty directory
 		 */

src/diff_file.c

@@ -320,7 +320,8 @@ static int diff_file_content_load_workdir_file(
 
 		error = git_filter_list_apply_to_data(&out, fl, &raw);
 
-		git_buf_free(&raw);
+		if (out.ptr != raw.ptr)
+			git_buf_free(&raw);
 
 		if (!error) {
 			fc->map.len  = out.size;

src/submodule.c

@@ -77,12 +77,12 @@ __KHASH_IMPL(
 	str, static kh_inline, const char *, void *, 1,
 	str_hash_no_trailing_slash, str_equal_no_trailing_slash);
 
-static int load_submodule_config(git_repository *repo);
+static int load_submodule_config(git_repository *repo, bool reload);
 static git_config_backend *open_gitmodules(git_repository *, bool, const git_oid *);
 static int lookup_head_remote(git_buf *url, git_repository *repo);
 static int submodule_get(git_submodule **, git_repository *, const char *, const char *);
 static int submodule_load_from_config(const git_config_entry *, void *);
-static int submodule_load_from_wd_lite(git_submodule *, const char *, void *);
+static int submodule_load_from_wd_lite(git_submodule *);
 static int submodule_update_config(git_submodule *, const char *, const char *, bool, bool);
 static void submodule_get_index_status(unsigned int *, git_submodule *);
 static void submodule_get_wd_status(unsigned int *, git_submodule *, git_repository *, git_submodule_ignore_t);
@@ -144,7 +144,7 @@ int git_submodule_lookup(
 
 	assert(repo && name);
 
-	if ((error = load_submodule_config(repo)) < 0)
+	if ((error = load_submodule_config(repo, false)) < 0)
 		return error;
 
 	if ((error = submodule_lookup(out, repo->submodules, name, NULL)) < 0) {
@@ -182,7 +182,7 @@ int git_submodule_foreach(
 
 	assert(repo && callback);
 
-	if ((error = load_submodule_config(repo)) < 0)
+	if ((error = load_submodule_config(repo, true)) < 0)
 		return error;
 
 	git_strmap_foreach_value(repo->submodules, sm, {
@@ -221,7 +221,10 @@ void git_submodule_config_free(git_repository *repo)
 	if (smcfg == NULL)
 		return;
 
-	git_strmap_foreach_value(smcfg, sm, { git_submodule_free(sm); });
+	git_strmap_foreach_value(smcfg, sm, {
+		sm->repo = NULL; /* disconnect from repo */;
+		git_submodule_free(sm);
+	});
 	git_strmap_free(smcfg);
 }
 
@@ -803,12 +806,60 @@ int git_submodule_open(git_repository **subrepo, git_submodule *sm)
 	return git_submodule__open(subrepo, sm, false);
 }
 
+static void submodule_cache_remove_item(
+	git_strmap *cache,
+	const char *name,
+	git_submodule *expected,
+	bool free_after_remove)
+{
+	khiter_t pos;
+	git_submodule *found;
+
+	if (!cache)
+		return;
+
+	pos = git_strmap_lookup_index(cache, name);
+
+	if (!git_strmap_valid_index(cache, pos))
+		return;
+
+	found = git_strmap_value_at(cache, pos);
+
+	if (expected && found != expected)
+		return;
+
+	git_strmap_set_value_at(cache, pos, NULL);
+	git_strmap_delete_at(cache, pos);
+
+	if (free_after_remove)
+		git_submodule_free(found);
+}
+
 int git_submodule_reload_all(git_repository *repo, int force)
 {
+	int error = 0;
+	git_submodule *sm;
+
 	GIT_UNUSED(force);
 	assert(repo);
-	git_submodule_config_free(repo);
-	return load_submodule_config(repo);
+
+	if (repo->submodules)
+		git_strmap_foreach_value(repo->submodules, sm, { sm->flags = 0; });
+
+	error = load_submodule_config(repo, true);
+
+	git_strmap_foreach_value(repo->submodules, sm, {
+		git_strmap *cache = repo->submodules;
+
+		if ((sm->flags & GIT_SUBMODULE_STATUS__IN_FLAGS) == 0) {
+			submodule_cache_remove_item(cache, sm->name, sm, true);
+
+			if (sm->path != sm->name)
+				submodule_cache_remove_item(cache, sm->path, sm, true);
+		}
+	});
+
+	return error;
 }
 
 static void submodule_update_from_index_entry(
@@ -884,6 +935,7 @@ static int submodule_update_head(git_submodule *submodule)
 	return 0;
 }
 
+
 int git_submodule_reload(git_submodule *submodule, int force)
 {
 	int error = 0;
@@ -901,6 +953,10 @@ int git_submodule_reload(git_submodule *submodule, int force)
 	if ((error = submodule_update_head(submodule)) < 0)
 		return error;
 
+	/* done if bare */
+	if (git_repository_is_bare(submodule->repo))
+		return error;
+
 	/* refresh config data */
 	mods = open_gitmodules(submodule->repo, false, NULL);
 	if (mods != NULL) {
@@ -924,11 +980,9 @@ int git_submodule_reload(git_submodule *submodule, int force)
 	}
 
 	/* refresh wd data */
-	submodule->flags = submodule->flags &
-		~(GIT_SUBMODULE_STATUS_IN_WD | GIT_SUBMODULE_STATUS__WD_OID_VALID);
+	submodule->flags &= ~GIT_SUBMODULE_STATUS__ALL_WD_FLAGS;
 
-	return submodule_load_from_wd_lite(
-		submodule, submodule->path, submodule->repo);
+	return submodule_load_from_wd_lite(submodule);
 }
 
 static void submodule_copy_oid_maybe(
@@ -1057,6 +1111,13 @@ static void submodule_release(git_submodule *sm)
 	if (!sm)
 		return;
 
+	if (sm->repo) {
+		git_strmap *cache = sm->repo->submodules;
+		submodule_cache_remove_item(cache, sm->name, sm, false);
+		if (sm->path != sm->name)
+			submodule_cache_remove_item(cache, sm->path, sm, false);
+	}
+
 	if (sm->path != sm->name)
 		git__free(sm->path);
 	git__free(sm->name);
@@ -1265,8 +1326,8 @@ static int submodule_load_from_config(
 		sm->update_default = sm->update;
 	}
 	else if (strcasecmp(property, "fetchRecurseSubmodules") == 0) {
-		if (git_submodule_parse_recurse(&sm->fetch_recurse, value) < 0)
-			return -1;
+		if ((error = git_submodule_parse_recurse(&sm->fetch_recurse, value)) < 0)
+			goto done;
 		sm->fetch_recurse_default = sm->fetch_recurse;
 	}
 	else if (strcasecmp(property, "ignore") == 0) {
@@ -1282,16 +1343,10 @@ done:
 	return error;
 }
 
-static int submodule_load_from_wd_lite(
-	git_submodule *sm, const char *name, void *payload)
+static int submodule_load_from_wd_lite(git_submodule *sm)
 {
 	git_buf path = GIT_BUF_INIT;
 
-	GIT_UNUSED(name); GIT_UNUSED(payload);
-
-	if (git_repository_is_bare(sm->repo))
-		return 0;
-
 	if (git_buf_joinpath(&path, git_repository_workdir(sm->repo), sm->path) < 0)
 		return -1;
 
@@ -1435,13 +1490,13 @@ static git_config_backend *open_gitmodules(
 	return mods;
 }
 
-static int load_submodule_config(git_repository *repo)
+static int load_submodule_config(git_repository *repo, bool reload)
 {
 	int error;
 	git_oid gitmodules_oid;
 	git_config_backend *mods = NULL;
 
-	if (repo->submodules)
+	if (!reload && repo->submodules)
 		return 0;
 
 	memset(&gitmodules_oid, 0, sizeof(gitmodules_oid));
@@ -1454,6 +1509,8 @@ static int load_submodule_config(git_repository *repo)
 		GITERR_CHECK_ALLOC(repo->submodules);
 	}
 
+	/* TODO: only do the following if the sources appear modified */
+
 	/* add submodule information from index */
 
 	if ((error = load_submodule_config_from_index(repo, &gitmodules_oid)) < 0)
@@ -1473,8 +1530,16 @@ static int load_submodule_config(git_repository *repo)
 
 	/* shallow scan submodules in work tree */
 
-	if (!git_repository_is_bare(repo))
-		error = git_submodule_foreach(repo, submodule_load_from_wd_lite, NULL);
+	if (!git_repository_is_bare(repo)) {
+		git_submodule *sm;
+
+		git_strmap_foreach_value(repo->submodules, sm, {
+			sm->flags &= ~GIT_SUBMODULE_STATUS__ALL_WD_FLAGS;
+		});
+		git_strmap_foreach_value(repo->submodules, sm, {
+			submodule_load_from_wd_lite(sm);
+		});
+	}
 
 cleanup:
 	if (mods != NULL)

src/submodule.h

@@ -111,6 +111,11 @@ enum {
 	GIT_SUBMODULE_STATUS__INDEX_MULTIPLE_ENTRIES = (1u << 27),
 };
 
+#define GIT_SUBMODULE_STATUS__ALL_WD_FLAGS \
+	(GIT_SUBMODULE_STATUS_IN_WD | \
+	 GIT_SUBMODULE_STATUS__WD_OID_VALID | \
+	 GIT_SUBMODULE_STATUS__WD_FLAGS)
+
 #define GIT_SUBMODULE_STATUS__CLEAR_INTERNAL(S) \
 	((S) & ~(0xFFFFFFFFu << 20))