18 files changed, 157 insertions, 103 deletions

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c0a819ed7..243b696d7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,10 @@ v0.23 + 1
 
 * `git_cert` descendent types now have a proper `parent` member
 
+* It is the responsibility fo the refdb backend to decide what to do
+  with the reflog on ref deletion. The file-based backend must delete
+  it, a database-backed one may wish to archive it.
+
 v0.23
 ------
 
diff --git a/examples/network/fetch.c b/examples/network/fetch.c
index 6be12406b..bc7a5a05e 100644
--- a/examples/network/fetch.c
+++ b/examples/network/fetch.c
@@ -23,32 +23,6 @@ static int progress_cb(const char *str, int len, void *data)
 	return 0;
 }
 
-static void *download(void *ptr)
-{
-	struct dl_data *data = (struct dl_data *)ptr;
-
-	// Connect to the remote end specifying that we want to fetch
-	// information from it.
-	if (git_remote_connect(data->remote, GIT_DIRECTION_FETCH, &data->fetch_opts->callbacks) < 0) {
-		data->ret = -1;
-		goto exit;
-	}
-
-	// Download the packfile and index it. This function updates the
-	// amount of received data and the indexer stats which lets you
-	// inform the user about progress.
-	if (git_remote_download(data->remote, NULL, data->fetch_opts) < 0) {
-		data->ret = -1;
-		goto exit;
-	}
-
-	data->ret = 0;
-
-exit:
-	data->finished = 1;
-	return &data->ret;
-}
-
 /**
  * This function gets called for each remote-tracking branch that gets
  * updated. The message we output depends on whether it's a new one or
@@ -73,6 +47,24 @@ static int update_cb(const char *refname, const git_oid *a, const git_oid *b, vo
 	return 0;
 }
 
+/**
+ * This gets called during the download and indexing. Here we show
+ * processed and total objects in the pack and the amount of received
+ * data. Most frontends will probably want to show a percentage and
+ * the download rate.
+ */
+static int transfer_progress_cb(const git_transfer_progress *stats, void *payload)
+{
+	if (stats->received_objects == stats->total_objects) {
+		printf("Resolving deltas %d/%d\r",
+		       stats->indexed_deltas, stats->total_deltas);
+	} else if (stats->total_objects > 0) {
+		printf("Received %d/%d objects (%d) in %" PRIuZ " bytes\r",
+		       stats->received_objects, stats->total_objects,
+		       stats->indexed_objects, stats->received_bytes);
+	}
+}
+
 /** Entry point for this command */
 int fetch(git_repository *repo, int argc, char **argv)
 {
@@ -80,9 +72,6 @@ int fetch(git_repository *repo, int argc, char **argv)
 	const git_transfer_progress *stats;
 	struct dl_data data;
 	git_fetch_options fetch_opts = GIT_FETCH_OPTIONS_INIT;
-#ifndef _WIN32
-	pthread_t worker;
-#endif
 
 	if (argc < 2) {
 		fprintf(stderr, "usage: %s fetch <repo>\n", argv[-1]);
@@ -99,49 +88,23 @@ int fetch(git_repository *repo, int argc, char **argv)
 	// Set up the callbacks (only update_tips for now)
 	fetch_opts.callbacks.update_tips = &update_cb;
 	fetch_opts.callbacks.sideband_progress = &progress_cb;
+	fetch_opts.callbacks.transfer_progress = transfer_progress_cb;
 	fetch_opts.callbacks.credentials = cred_acquire_cb;
 
-	// Set up the information for the background worker thread
-	data.remote = remote;
-	data.fetch_opts = &fetch_opts;
-	data.ret = 0;
-	data.finished = 0;
-
-	stats = git_remote_stats(remote);
-
-#ifdef _WIN32
-	download(&data);
-#else
-	pthread_create(&worker, NULL, download, &data);
-
-	// Loop while the worker thread is still running. Here we show processed
-	// and total objects in the pack and the amount of received
-	// data. Most frontends will probably want to show a percentage and
-	// the download rate.
-	do {
-		usleep(10000);
-
-		if (stats->received_objects == stats->total_objects) {
-			printf("Resolving deltas %d/%d\r",
-			       stats->indexed_deltas, stats->total_deltas);
-		} else if (stats->total_objects > 0) {
-			printf("Received %d/%d objects (%d) in %" PRIuZ " bytes\r",
-			       stats->received_objects, stats->total_objects,
-				   stats->indexed_objects, stats->received_bytes);
-		}
-	} while (!data.finished);
-
-	if (data.ret < 0)
-		goto on_error;
-
-	pthread_join(worker, NULL);
-#endif
+	/**
+	 * Perform the fetch with the configured refspecs from the
+	 * config. Update the reflog for the updated references with
+	 * "fetch".
+	 */
+	if (git_remote_fetch(remote, NULL, &fetch_opts, "fetch") < 0)
+		return -1;
 
 	/**
 	 * If there are local objects (we got a thin pack), then tell
 	 * the user how many objects we saved from having to cross the
 	 * network.
 	 */
+	stats = git_remote_stats(remote);
 	if (stats->local_objects > 0) {
 		printf("\rReceived %d/%d objects in %" PRIuZ " bytes (used %d local objects)\n",
 		       stats->indexed_objects, stats->total_objects, stats->received_bytes, stats->local_objects);
@@ -150,16 +113,6 @@ int fetch(git_repository *repo, int argc, char **argv)
 			stats->indexed_objects, stats->total_objects, stats->received_bytes);
 	}
 
-	// Disconnect the underlying connection to prevent from idling.
-	git_remote_disconnect(remote);
-
-	// Update the references in the remote's namespace to point to the
-	// right commits. This may be needed even if there was no packfile
-	// to download, which can happen e.g. when the branches have been
-	// changed but all the needed objects are available locally.
-	if (git_remote_update_tips(remote, &fetch_opts.callbacks, 1, fetch_opts.download_tags, NULL) < 0)
-		return -1;
-
 	git_remote_free(remote);
 
 	return 0;
diff --git a/include/git2/errors.h b/include/git2/errors.h
index a81aa05d9..e189e55f1 100644
--- a/include/git2/errors.h
+++ b/include/git2/errors.h
@@ -48,6 +48,7 @@ typedef enum {
 	GIT_EEOF            = -20,      /**< Unexpected EOF */
 	GIT_EINVALID        = -21,      /**< Invalid operation or input */
 	GIT_EUNCOMMITTED    = -22,	/**< Uncommitted changes in index prevented operation */
+	GIT_EDIRECTORY      = -23,      /**< The operation is not valid for a directory */
 
 	GIT_PASSTHROUGH     = -30,	/**< Internal only */
 	GIT_ITEROVER        = -31,	/**< Signals end of iteration with iterator */
diff --git a/include/git2/remote.h b/include/git2/remote.h
index e47f00881..444fe5276 100644
--- a/include/git2/remote.h
+++ b/include/git2/remote.h
@@ -511,6 +511,14 @@ typedef enum {
 	GIT_REMOTE_DOWNLOAD_TAGS_ALL,
 } git_remote_autotag_option_t;
 
+/**
+ * Fetch options structure.
+ *
+ * Zero out for defaults.  Initialize with `GIT_FETCH_OPTIONS_INIT` macro to
+ * correctly set the `version` field.  E.g.
+ *
+ *		git_fetch_options opts = GIT_FETCH_OPTIONS_INIT;
+ */
 typedef struct {
 	int version;
 
@@ -739,7 +747,7 @@ GIT_EXTERN(int) git_remote_prune_refs(const git_remote *remote);
  * stored here for further processing by the caller. Always free this
  * strarray on successful return.
  * @param repo the repository in which to rename
- * @param name the current name of the reamote
+ * @param name the current name of the remote
  * @param new_name the new name the remote should bear
  * @return 0, GIT_EINVALIDSPEC, GIT_EEXISTS or an error code
  */
diff --git a/include/git2/sys/refdb_backend.h b/include/git2/sys/refdb_backend.h
index d943e550f..9f2a99b7e 100644
--- a/include/git2/sys/refdb_backend.h
+++ b/include/git2/sys/refdb_backend.h
@@ -103,8 +103,9 @@ struct git_refdb_backend {
 		const git_signature *who, const char *message);
 
 	/**
-	 * Deletes the given reference from the refdb.  A refdb implementation
-	 * must provide this function.
+	 * Deletes the given reference (and if necessary its reflog)
+	 * from the refdb.  A refdb implementation must provide this
+	 * function.
 	 */
 	int (*del)(git_refdb_backend *backend, const char *ref_name, const git_oid *old_id, const char *old_target);
 
diff --git a/src/blob.c b/src/blob.c
index 07c4d92c8..ad0f4ac62 100644
--- a/src/blob.c
+++ b/src/blob.c
@@ -185,6 +185,12 @@ int git_blob__create_from_paths(
 		(error = git_repository_odb(&odb, repo)) < 0)
 		goto done;
 
+	if (S_ISDIR(st.st_mode)) {
+		giterr_set(GITERR_ODB, "cannot create blob from '%s'; it is a directory", content_path);
+		error = GIT_EDIRECTORY;
+		goto done;
+	}
+
 	if (out_st)
 		memcpy(out_st, &st, sizeof(st));
 
diff --git a/src/branch.c b/src/branch.c
index 791d55106..0dcc14c29 100644
--- a/src/branch.c
+++ b/src/branch.c
@@ -155,18 +155,7 @@ int git_branch_delete(git_reference *branch)
 		git_reference_owner(branch), git_buf_cstr(&config_section), NULL) < 0)
 		goto on_error;
 
-	if (git_reference_delete(branch) < 0)
-		goto on_error;
-
-	if ((error = git_reflog_delete(git_reference_owner(branch), git_reference_name(branch))) < 0) {
-		if (error == GIT_ENOTFOUND) {
-			giterr_clear();
-			error = 0;
-		}
-		goto on_error;
-	}
-
-	error = 0;
+	error = git_reference_delete(branch);
 
 on_error:
 	git_buf_free(&config_section);
diff --git a/src/filter.c b/src/filter.c
index 70c4fa382..60473e4e1 100644
--- a/src/filter.c
+++ b/src/filter.c
@@ -950,18 +950,20 @@ int git_filter_list_stream_data(
 {
 	git_vector filter_streams = GIT_VECTOR_INIT;
 	git_writestream *stream_start;
-	int error = 0;
+	int error = 0, close_error;
 
 	git_buf_sanitize(data);
 
-	if ((error = stream_list_init(
-			&stream_start, &filter_streams, filters, target)) == 0 &&
-		(error =
-			stream_start->write(stream_start, data->ptr, data->size)) == 0)
-		error = stream_start->close(stream_start);
+	if ((error = stream_list_init(&stream_start, &filter_streams, filters, target)) < 0)
+		goto out;
 
+	error = stream_start->write(stream_start, data->ptr, data->size);
+
+out:
+	close_error = stream_start->close(stream_start);
 	stream_list_free(&filter_streams);
-	return error;
+	/* propagate the stream init or write error */
+	return error < 0 ? error : close_error;
 }
 
 int git_filter_list_stream_blob(
diff --git a/src/global.c b/src/global.c
index fc6337adc..37a47bd27 100644
--- a/src/global.c
+++ b/src/global.c
@@ -344,8 +344,8 @@ int git_libgit2_init(void)
 {
 	int ret;
 
-	pthread_once(&_once_init, init_once);
 	ret = git_atomic_inc(&git__n_inits);
+	pthread_once(&_once_init, init_once);
 
 	return init_error ? init_error : ret;
 }
diff --git a/src/index.c b/src/index.c
index 5ce5522f8..501498e9e 100644
--- a/src/index.c
+++ b/src/index.c
@@ -1236,9 +1236,29 @@ int git_index_add_bypath(git_index *index, const char *path)
 
 	assert(index && path);
 
-	if ((ret = index_entry_init(&entry, index, path)) < 0 ||
-		(ret = index_insert(index, &entry, 1, false)) < 0)
+	if ((ret = index_entry_init(&entry, index, path)) == 0)
+		ret = index_insert(index, &entry, 1, false);
+
+	/* If we were given a directory, let's see if it's a submodule */
+	if (ret < 0 && ret != GIT_EDIRECTORY)
+		return ret;
+
+	if (ret == GIT_EDIRECTORY) {
+		git_submodule *sm;
+		git_error_state err;
+
+		giterr_capture(&err, ret);
+
+		ret = git_submodule_lookup(&sm, INDEX_OWNER(index), path);
+		if (ret == GIT_ENOTFOUND)
+			return giterr_restore(&err);
+		else
+			git__free(err.error_msg.message);
+
+		ret = git_submodule_add_to_index(sm, false);
+		git_submodule_free(sm);
 		return ret;
+	}
 
 	/* Adding implies conflict was resolved, move conflict entries to REUC */
 	if ((ret = index_conflict_to_reuc(index, path)) < 0 && ret != GIT_ENOTFOUND)
diff --git a/src/path.c b/src/path.c
index 16283cab2..8317aaaa7 100644
--- a/src/path.c
+++ b/src/path.c
@@ -12,6 +12,7 @@
 #include "win32/posix.h"
 #include "win32/buffer.h"
 #include "win32/w32_util.h"
+#include "win32/version.h"
 #else
 #include <dirent.h>
 #endif
@@ -1085,7 +1086,7 @@ int git_path_direach(
 #if defined(GIT_WIN32) && !defined(__MINGW32__)
 
 /* Using _FIND_FIRST_EX_LARGE_FETCH may increase performance in Windows 7
- * and better.  Prior versions will ignore this.
+ * and better.
  */
 #ifndef FIND_FIRST_EX_LARGE_FETCH
 # define FIND_FIRST_EX_LARGE_FETCH 2
@@ -1099,6 +1100,10 @@ int git_path_diriter_init(
 	git_win32_path path_filter;
 	git_buf hack = {0};
 
+	static int is_win7_or_later = -1;
+	if (is_win7_or_later < 0)
+		is_win7_or_later = git_has_win32_version(6, 1, 0);
+
 	assert(diriter && path);
 
 	memset(diriter, 0, sizeof(git_path_diriter));
@@ -1122,11 +1127,11 @@ int git_path_diriter_init(
 
 	diriter->handle = FindFirstFileExW(
 		path_filter,
-		FindExInfoBasic,
+		is_win7_or_later ? FindExInfoBasic : FindExInfoStandard,
 		&diriter->current,
 		FindExSearchNameMatch,
 		NULL,
-		FIND_FIRST_EX_LARGE_FETCH);
+		is_win7_or_later ? FIND_FIRST_EX_LARGE_FETCH : 0);
 
 	if (diriter->handle == INVALID_HANDLE_VALUE) {
 		giterr_set(GITERR_OS, "Could not open directory '%s'", path);
diff --git a/src/refdb_fs.c b/src/refdb_fs.c
index e1a77f3ff..55d535eb4 100644
--- a/src/refdb_fs.c
+++ b/src/refdb_fs.c
@@ -63,6 +63,8 @@ typedef struct refdb_fs_backend {
 	uint32_t direach_flags;
 } refdb_fs_backend;
 
+static int refdb_reflog_fs__delete(git_refdb_backend *_backend, const char *name);
+
 static int packref_cmp(const void *a_, const void *b_)
 {
 	const struct packref *a = a_, *b = b_;
@@ -1217,6 +1219,11 @@ static int refdb_fs_backend__delete(
 	if ((error = loose_lock(&file, backend, ref_name)) < 0)
 		return error;
 
+	if ((error = refdb_reflog_fs__delete(_backend, ref_name)) < 0) {
+		git_filebuf_cleanup(&file);
+		return error;
+	}
+
 	return refdb_fs_backend__delete_tail(_backend, &file, ref_name, old_id, old_target);
 }
 
diff --git a/src/submodule.c b/src/submodule.c
index f16d3c5ab..991ebc8f3 100644
--- a/src/submodule.c
+++ b/src/submodule.c
@@ -1658,7 +1658,7 @@ static int submodule_load_from_config(
 	} else {
 		khiter_t pos;
 		git_strmap *map = data->map;
-		pos = git_strmap_lookup_index(map, name.ptr);
+		pos = git_strmap_lookup_index(map, path ? path : name.ptr);
 		if (git_strmap_valid_index(map, pos)) {
 			sm = git_strmap_value_at(map, pos);
 		} else {
diff --git a/src/thread-utils.c b/src/thread-utils.c
index c3baf411a..dc9b2f09e 100644
--- a/src/thread-utils.c
+++ b/src/thread-utils.c
@@ -8,7 +8,9 @@
 #include "thread-utils.h"
 
 #ifdef _WIN32
+#ifndef WIN32_LEAN_AND_MEAN
 #	define WIN32_LEAN_AND_MEAN
+#endif
 #	include <windows.h>
 #elif defined(hpux) || defined(__hpux) || defined(_hpux)
 #	include <sys/pstat.h>
diff --git a/tests/index/bypath.c b/tests/index/bypath.c
new file mode 100644
index 000000000..ddb766a22
--- /dev/null
+++ b/tests/index/bypath.c
@@ -0,0 +1,35 @@
+#include "clar_libgit2.h"
+#include "repository.h"
+#include "../submodule/submodule_helpers.h"
+
+static git_repository *g_repo;
+static git_index *g_idx;
+
+void test_index_bypath__initialize(void)
+{
+	g_repo = setup_fixture_submod2();
+	cl_git_pass(git_repository_index__weakptr(&g_idx, g_repo));
+}
+
+void test_index_bypath__cleanup(void)
+{
+	g_repo = NULL;
+	g_idx = NULL;
+}
+
+void test_index_bypath__add_directory(void)
+{
+	cl_git_fail_with(GIT_EDIRECTORY, git_index_add_bypath(g_idx, "just_a_dir"));
+}
+
+void test_index_bypath__add_submodule(void)
+{
+	unsigned int status;
+	const char *sm_name = "sm_changed_head";
+
+	cl_git_pass(git_submodule_status(&status, g_repo, sm_name, 0));
+	cl_assert_equal_i(GIT_SUBMODULE_STATUS_WD_MODIFIED, status & GIT_SUBMODULE_STATUS_WD_MODIFIED);
+	cl_git_pass(git_index_add_bypath(g_idx, sm_name));
+	cl_git_pass(git_submodule_status(&status, g_repo, sm_name, 0));
+	cl_assert_equal_i(0, status & GIT_SUBMODULE_STATUS_WD_MODIFIED);
+}
diff --git a/tests/refs/branches/delete.c b/tests/refs/branches/delete.c
index 343ff0f50..8807db231 100644
--- a/tests/refs/branches/delete.c
+++ b/tests/refs/branches/delete.c
@@ -132,6 +132,8 @@ void test_refs_branches_delete__removes_reflog(void)
 	cl_git_pass(git_branch_delete(branch));
 	git_reference_free(branch);
 
+	cl_assert_equal_i(false, git_reference_has_log(repo, "refs/heads/track-local"));
+
 	/* Reading a nonexistant reflog creates it, but it should be empty */
 	cl_git_pass(git_reflog_read(&log, repo, "refs/heads/track-local"));
 	cl_assert_equal_i(0, git_reflog_entrycount(log));
diff --git a/tests/submodule/add.c b/tests/submodule/add.c
index 01625d3aa..c3b3e6364 100644
--- a/tests/submodule/add.c
+++ b/tests/submodule/add.c
@@ -4,6 +4,7 @@
 #include "submodule_helpers.h"
 #include "config/config_helpers.h"
 #include "fileops.h"
+#include "repository.h"
 
 static git_repository *g_repo = NULL;
 
diff --git a/tests/submodule/lookup.c b/tests/submodule/lookup.c
index 38f06abbc..ecea694e5 100644
--- a/tests/submodule/lookup.c
+++ b/tests/submodule/lookup.c
@@ -1,6 +1,7 @@
 #include "clar_libgit2.h"
 #include "submodule_helpers.h"
 #include "git2/sys/repository.h"
+#include "repository.h"
 #include "fileops.h"
 
 static git_repository *g_repo = NULL;
@@ -103,8 +104,25 @@ static int sm_lookup_cb(git_submodule *sm, const char *name, void *payload)
 
 void test_submodule_lookup__foreach(void)
 {
+	git_config *cfg;
 	sm_lookup_data data;
+
+	memset(&data, 0, sizeof(data));
+	cl_git_pass(git_submodule_foreach(g_repo, sm_lookup_cb, &data));
+	cl_assert_equal_i(8, data.count);
+
 	memset(&data, 0, sizeof(data));
+
+	/* Change the path for a submodule so it doesn't match the name */
+	cl_git_pass(git_config_open_ondisk(&cfg, "submod2/.gitmodules"));
+
+	cl_git_pass(git_config_set_string(cfg, "submodule.smchangedindex.path", "sm_changed_index"));
+	cl_git_pass(git_config_set_string(cfg, "submodule.smchangedindex.url", "../submod2_target"));
+	cl_git_pass(git_config_delete_entry(cfg, "submodule.sm_changed_index.path"));
+	cl_git_pass(git_config_delete_entry(cfg, "submodule.sm_changed_index.url"));
+
+	git_config_free(cfg);
+
 	cl_git_pass(git_submodule_foreach(g_repo, sm_lookup_cb, &data));
 	cl_assert_equal_i(8, data.count);
 }