thodg/libgit2

diff --git a/include/git2.h b/include/git2.h
index f749760..d843539 100644
--- a/include/git2.h
+++ b/include/git2.h
@@ -32,6 +32,7 @@
 #include "git2/notes.h"
 #include "git2/object.h"
 #include "git2/odb.h"
+#include "git2/odb_backend.h"
 #include "git2/oid.h"
 #include "git2/pack.h"
 #include "git2/patch.h"
diff --git a/src/cc-compat.h b/src/cc-compat.h
index e73cb6d..0b66d8b 100644
--- a/src/cc-compat.h
+++ b/src/cc-compat.h
@@ -35,6 +35,14 @@
 #	define GIT_TYPEOF(x)
 #endif
 
+#if defined(__GNUC__)
+#	define GIT_ALIGN(x,size) x __attribute__ ((aligned(size)))
+#elif defined(_MSC_VER)
+#	define GIT_ALIGN(x,size) __declspec(align(size)) x
+#else
+#	define GIT_ALIGN(x,size) x
+#endif
+
 #define GIT_UNUSED(x) ((void)(x))
 
 /* Define the printf format specifer to use for size_t output */
diff --git a/src/config_file.c b/src/config_file.c
index 7106f18..8f55c42 100644
--- a/src/config_file.c
+++ b/src/config_file.c
@@ -1163,7 +1163,7 @@ static int strip_comments(char *line, int in_quotes)
 	}
 
 	/* skip any space at the end */
-	if (ptr > line && git__isspace(ptr[-1])) {
+	while (ptr > line && git__isspace(ptr[-1])) {
 		ptr--;
 	}
 	ptr[0] = '\0';
diff --git a/src/diff_patch.c b/src/diff_patch.c
index 38d5f42..4e0672a 100644
--- a/src/diff_patch.c
+++ b/src/diff_patch.c
@@ -274,6 +274,7 @@ int git_diff_foreach(
 		return error;
 
 	memset(&xo, 0, sizeof(xo));
+	memset(&patch, 0, sizeof(patch));
 	diff_output_init(
 		&xo.output, &diff->opts, file_cb, hunk_cb, data_cb, payload);
 	git_xdiff_init(&xo, &diff->opts);
diff --git a/src/filter.c b/src/filter.c
index b9e4f9e..b5a8bdd 100644
--- a/src/filter.c
+++ b/src/filter.c
@@ -38,7 +38,7 @@ struct git_filter_list {
 };
 
 typedef struct {
-	const char *filter_name;
+	char *filter_name;
 	git_filter *filter;
 	int priority;
 	int initialized;
@@ -75,6 +75,7 @@ static void filter_registry_shutdown(void)
 			fdef->initialized = false;
 		}
 
+		git__free(fdef->filter_name);
 		git__free(fdef->attrdata);
 		git__free(fdef);
 	}
@@ -230,6 +231,8 @@ int git_filter_register(
 	size_t nattr = 0, nmatch = 0;
 	git_buf attrs = GIT_BUF_INIT;
 
+	assert(name && filter);
+
 	if (filter_registry_initialize() < 0)
 		return -1;
 
@@ -246,7 +249,9 @@ int git_filter_register(
 		sizeof(git_filter_def) + 2 * nattr * sizeof(char *), 1);
 	GITERR_CHECK_ALLOC(fdef);
 
-	fdef->filter_name = name;
+	fdef->filter_name = git__strdup(name);
+	GITERR_CHECK_ALLOC(fdef->filter_name);
+
 	fdef->filter      = filter;
 	fdef->priority    = priority;
 	fdef->nattrs      = nattr;
@@ -256,6 +261,7 @@ int git_filter_register(
 	filter_def_set_attrs(fdef);
 
 	if (git_vector_insert(&git__filter_registry->filters, fdef) < 0) {
+		git__free(fdef->filter_name);
 		git__free(fdef->attrdata);
 		git__free(fdef);
 		return -1;
@@ -270,6 +276,8 @@ int git_filter_unregister(const char *name)
 	size_t pos;
 	git_filter_def *fdef;
 
+	assert(name);
+
 	/* cannot unregister default filters */
 	if (!strcmp(GIT_FILTER_CRLF, name) || !strcmp(GIT_FILTER_IDENT, name)) {
 		giterr_set(GITERR_FILTER, "Cannot unregister filter '%s'", name);
@@ -288,6 +296,7 @@ int git_filter_unregister(const char *name)
 		fdef->initialized = false;
 	}
 
+	git__free(fdef->filter_name);
 	git__free(fdef->attrdata);
 	git__free(fdef);
 
diff --git a/src/global.c b/src/global.c
index c72bfe8..5e703e6 100644
--- a/src/global.c
+++ b/src/global.c
@@ -221,6 +221,9 @@ int init_error = 0;
 
 static void cb__free_status(void *st)
 {
+	git_global_st *state = (git_global_st *) st;
+	git__free(state->error_t.message);
+
 	git__free(st);
 }
 
diff --git a/src/index.c b/src/index.c
index b63a0be..8b757f2 100644
--- a/src/index.c
+++ b/src/index.c
@@ -1767,35 +1767,42 @@ static size_t read_entry(
 	git_index_entry **out, const void *buffer, size_t buffer_size)
 {
 	size_t path_length, entry_size;
-	uint16_t flags_raw;
 	const char *path_ptr;
-	const struct entry_short *source = buffer;
+	struct entry_short source;
 	git_index_entry entry = {{0}};
 
 	if (INDEX_FOOTER_SIZE + minimal_entry_size > buffer_size)
 		return 0;
 
-	entry.ctime.seconds = (git_time_t)ntohl(source->ctime.seconds);
-	entry.ctime.nanoseconds = ntohl(source->ctime.nanoseconds);
-	entry.mtime.seconds = (git_time_t)ntohl(source->mtime.seconds);
-	entry.mtime.nanoseconds = ntohl(source->mtime.nanoseconds);
-	entry.dev = ntohl(source->dev);
-	entry.ino = ntohl(source->ino);
-	entry.mode = ntohl(source->mode);
-	entry.uid = ntohl(source->uid);
-	entry.gid = ntohl(source->gid);
-	entry.file_size = ntohl(source->file_size);
-	git_oid_cpy(&entry.id, &source->oid);
-	entry.flags = ntohs(source->flags);
+	/* buffer is not guaranteed to be aligned */
+	memcpy(&source, buffer, sizeof(struct entry_short));
+
+	entry.ctime.seconds = (git_time_t)ntohl(source.ctime.seconds);
+	entry.ctime.nanoseconds = ntohl(source.ctime.nanoseconds);
+	entry.mtime.seconds = (git_time_t)ntohl(source.mtime.seconds);
+	entry.mtime.nanoseconds = ntohl(source.mtime.nanoseconds);
+	entry.dev = ntohl(source.dev);
+	entry.ino = ntohl(source.ino);
+	entry.mode = ntohl(source.mode);
+	entry.uid = ntohl(source.uid);
+	entry.gid = ntohl(source.gid);
+	entry.file_size = ntohl(source.file_size);
+	git_oid_cpy(&entry.id, &source.oid);
+	entry.flags = ntohs(source.flags);
 
 	if (entry.flags & GIT_IDXENTRY_EXTENDED) {
-		const struct entry_long *source_l = (const struct entry_long *)source;
-		path_ptr = source_l->path;
+		uint16_t flags_raw;
+		size_t flags_offset;
 
-		flags_raw = ntohs(source_l->flags_extended);
-		memcpy(&entry.flags_extended, &flags_raw, 2);
+		flags_offset = offsetof(struct entry_long, flags_extended);
+		memcpy(&flags_raw, (const char *) buffer + flags_offset,
+			sizeof(flags_raw));
+		flags_raw = ntohs(flags_raw);
+
+		memcpy(&entry.flags_extended, &flags_raw, sizeof(flags_raw));
+		path_ptr = (const char *) buffer + offsetof(struct entry_long, path);
 	} else
-		path_ptr = source->path;
+		path_ptr = (const char *) buffer + offsetof(struct entry_short, path);
 
 	path_length = entry.flags & GIT_IDXENTRY_NAMEMASK;
 
@@ -1846,14 +1853,12 @@ static int read_header(struct index_header *dest, const void *buffer)
 
 static size_t read_extension(git_index *index, const char *buffer, size_t buffer_size)
 {
-	const struct index_extension *source;
 	struct index_extension dest;
 	size_t total_size;
 
-	source = (const struct index_extension *)(buffer);
-
-	memcpy(dest.signature, source->signature, 4);
-	dest.extension_size = ntohl(source->extension_size);
+	/* buffer is not guaranteed to be aligned */
+	memcpy(&dest, buffer, sizeof(struct index_extension));
+	dest.extension_size = ntohl(dest.extension_size);
 
 	total_size = dest.extension_size + sizeof(struct index_extension);
 
diff --git a/src/netops.c b/src/netops.c
index 8a60299..ea5d4ed 100644
--- a/src/netops.c
+++ b/src/netops.c
@@ -460,7 +460,7 @@ int gitno_connect(gitno_socket *s_out, const char *host, const char *port, int f
 	hints.ai_socktype = SOCK_STREAM;
 	hints.ai_family = AF_UNSPEC;
 
-	if ((ret = p_getaddrinfo(host, port, &hints, &info)) < 0) {
+	if ((ret = p_getaddrinfo(host, port, &hints, &info)) != 0) {
 		giterr_set(GITERR_NET,
 			"Failed to resolve address for %s: %s", host, p_gai_strerror(ret));
 		return -1;
diff --git a/src/pack.c b/src/pack.c
index 892eeb4..1325e21 100644
--- a/src/pack.c
+++ b/src/pack.c
@@ -620,7 +620,7 @@ int git_packfile_unpack(
 	struct pack_chain_elem *elem = NULL, *stack;
 	git_pack_cache_entry *cached = NULL;
 	struct pack_chain_elem small_stack[SMALL_STACK_SIZE];
-	size_t stack_size, elem_pos;
+	size_t stack_size = 0, elem_pos;
 	git_otype base_type;
 
 	/*
diff --git a/src/pool.c b/src/pool.c
index a516ff9..3055527 100644
--- a/src/pool.c
+++ b/src/pool.c
@@ -7,7 +7,7 @@ struct git_pool_page {
 	git_pool_page *next;
 	uint32_t size;
 	uint32_t avail;
-	char data[GIT_FLEX_ARRAY];
+	GIT_ALIGN(char data[GIT_FLEX_ARRAY], 8);
 };
 
 struct pool_freelist {
diff --git a/src/remote.c b/src/remote.c
index 740b201..aa70bb7 100644
--- a/src/remote.c
+++ b/src/remote.c
@@ -1057,16 +1057,20 @@ static int update_tips_for_spec(
 		if (autotag && !git_odb_exists(odb, &head->oid))
 			continue;
 
-		if (git_vector_insert(&update_heads, head) < 0)
+		if (!autotag && git_vector_insert(&update_heads, head) < 0)
 			goto on_error;
 
 		error = git_reference_name_to_id(&old, remote->repo, refname.ptr);
 		if (error < 0 && error != GIT_ENOTFOUND)
 			goto on_error;
 
-		if (error == GIT_ENOTFOUND)
+		if (error == GIT_ENOTFOUND) {
 			memset(&old, 0, GIT_OID_RAWSZ);
 
+			if (autotag && git_vector_insert(&update_heads, head) < 0)
+				goto on_error;
+		}
+
 		if (!git_oid__cmp(&old, &head->oid))
 			continue;
 
diff --git a/src/stash.c b/src/stash.c
index 86e0a62..4711ac7 100644
--- a/src/stash.c
+++ b/src/stash.c
@@ -232,7 +232,8 @@ static int build_untracked_tree(
 	}
 
 	if (flags & GIT_STASH_INCLUDE_IGNORED) {
-		opts.flags |= GIT_DIFF_INCLUDE_IGNORED;
+		opts.flags |= GIT_DIFF_INCLUDE_IGNORED |
+			GIT_DIFF_RECURSE_IGNORED_DIRS;
 		data.include_ignored = true;
 	}
 
@@ -447,10 +448,11 @@ static int ensure_there_are_changes_to_stash(
 
 	if (include_untracked_files)
 		opts.flags |= GIT_STATUS_OPT_INCLUDE_UNTRACKED |
-		GIT_STATUS_OPT_RECURSE_UNTRACKED_DIRS;
+			GIT_STATUS_OPT_RECURSE_UNTRACKED_DIRS;
 
 	if (include_ignored_files)
-		opts.flags |= GIT_STATUS_OPT_INCLUDE_IGNORED;
+		opts.flags |= GIT_STATUS_OPT_INCLUDE_IGNORED |
+			GIT_STATUS_OPT_RECURSE_IGNORED_DIRS;
 
 	error = git_status_foreach_ext(repo, &opts, is_dirty_cb, NULL);
 
diff --git a/tests/fetchhead/fetchhead_data.h b/tests/fetchhead/fetchhead_data.h
index 94402ab..c75b65b 100644
--- a/tests/fetchhead/fetchhead_data.h
+++ b/tests/fetchhead/fetchhead_data.h
@@ -16,6 +16,11 @@
 	"8f50ba15d49353813cc6e20298002c0d17b0a9ee\tnot-for-merge\ttag 'commit_tree' of git://github.com/libgit2/TestGitRepository\n" \
 	"6e0c7bdb9b4ed93212491ee778ca1c65047cab4e\tnot-for-merge\ttag 'nearly-dangling' of git://github.com/libgit2/TestGitRepository\n"
 
+#define FETCH_HEAD_WILDCARD_DATA2 \
+	"49322bb17d3acc9146f98c97d078513228bbf3c0\t\tbranch 'master' of git://github.com/libgit2/TestGitRepository\n" \
+	"0966a434eb1a025db6b71485ab63a3bfbea520b6\tnot-for-merge\tbranch 'first-merge' of git://github.com/libgit2/TestGitRepository\n" \
+	"42e4e7c5e507e113ebbb7801b16b52cf867b7ce1\tnot-for-merge\tbranch 'no-parent' of git://github.com/libgit2/TestGitRepository\n" \
+
 #define FETCH_HEAD_NO_MERGE_DATA \
 	"0966a434eb1a025db6b71485ab63a3bfbea520b6\tnot-for-merge\tbranch 'first-merge' of git://github.com/libgit2/TestGitRepository\n" \
 	"49322bb17d3acc9146f98c97d078513228bbf3c0\tnot-for-merge\tbranch 'master' of git://github.com/libgit2/TestGitRepository\n" \
@@ -25,6 +30,16 @@
 	"8f50ba15d49353813cc6e20298002c0d17b0a9ee\tnot-for-merge\ttag 'commit_tree' of git://github.com/libgit2/TestGitRepository\n" \
 	"6e0c7bdb9b4ed93212491ee778ca1c65047cab4e\tnot-for-merge\ttag 'nearly-dangling' of git://github.com/libgit2/TestGitRepository\n"
 
+#define FETCH_HEAD_NO_MERGE_DATA2 \
+	"0966a434eb1a025db6b71485ab63a3bfbea520b6\tnot-for-merge\tbranch 'first-merge' of git://github.com/libgit2/TestGitRepository\n" \
+	"49322bb17d3acc9146f98c97d078513228bbf3c0\tnot-for-merge\tbranch 'master' of git://github.com/libgit2/TestGitRepository\n" \
+	"42e4e7c5e507e113ebbb7801b16b52cf867b7ce1\tnot-for-merge\tbranch 'no-parent' of git://github.com/libgit2/TestGitRepository\n" \
+
+#define FETCH_HEAD_NO_MERGE_DATA3 \
+	"0966a434eb1a025db6b71485ab63a3bfbea520b6\tnot-for-merge\tbranch 'first-merge' of git://github.com/libgit2/TestGitRepository\n" \
+	"49322bb17d3acc9146f98c97d078513228bbf3c0\tnot-for-merge\tbranch 'master' of git://github.com/libgit2/TestGitRepository\n" \
+	"42e4e7c5e507e113ebbb7801b16b52cf867b7ce1\tnot-for-merge\tbranch 'no-parent' of git://github.com/libgit2/TestGitRepository\n" \
+	"8f50ba15d49353813cc6e20298002c0d17b0a9ee\tnot-for-merge\ttag 'commit_tree' of git://github.com/libgit2/TestGitRepository\n" \
 
 #define FETCH_HEAD_EXPLICIT_DATA \
 	"0966a434eb1a025db6b71485ab63a3bfbea520b6\t\tbranch 'first-merge' of git://github.com/libgit2/TestGitRepository\n"
diff --git a/tests/merge/merge_helpers.c b/tests/merge/merge_helpers.c
index 154985f..e3e7039 100644
--- a/tests/merge/merge_helpers.c
+++ b/tests/merge/merge_helpers.c
@@ -327,7 +327,7 @@ int merge_test_reuc(git_index *index, const struct merge_reuc_entry expected[], 
 
 int dircount(void *payload, git_buf *pathbuf)
 {
-	int *entries = payload;
+	size_t *entries = payload;
 	size_t len = git_buf_len(pathbuf);
 
 	if (len < 5 || strcmp(pathbuf->ptr + (git_buf_len(pathbuf) - 5), "/.git") != 0)
diff --git a/tests/odb/foreach.c b/tests/odb/foreach.c
index 56daf75..75448a2 100644
--- a/tests/odb/foreach.c
+++ b/tests/odb/foreach.c
@@ -87,7 +87,7 @@ void test_odb_foreach__files_in_objects_dir(void)
 	git_repository *repo;
 	git_odb *odb;
 	git_buf buf = GIT_BUF_INIT;
-	size_t nobj = 0;
+	int nobj = 0;
 
 	cl_fixture_sandbox("testrepo.git");
 	cl_git_pass(git_repository_open(&repo, "testrepo.git"));
diff --git a/tests/online/fetchhead.c b/tests/online/fetchhead.c
index 0b3f20d..3f27e13 100644
--- a/tests/online/fetchhead.c
+++ b/tests/online/fetchhead.c
@@ -67,6 +67,11 @@ static void fetchhead_test_fetch(const char *fetchspec, const char *expected_fet
 void test_online_fetchhead__wildcard_spec(void)
 {
 	fetchhead_test_clone();
+	fetchhead_test_fetch(NULL, FETCH_HEAD_WILDCARD_DATA2);
+	cl_git_pass(git_tag_delete(g_repo, "annotated_tag"));
+	cl_git_pass(git_tag_delete(g_repo, "blob"));
+	cl_git_pass(git_tag_delete(g_repo, "commit_tree"));
+	cl_git_pass(git_tag_delete(g_repo, "nearly-dangling"));
 	fetchhead_test_fetch(NULL, FETCH_HEAD_WILDCARD_DATA);
 }
 
@@ -87,5 +92,12 @@ void test_online_fetchhead__no_merges(void)
 	cl_git_pass(git_config_delete_entry(config, "branch.master.merge"));
 	git_config_free(config);
 
+	fetchhead_test_fetch(NULL, FETCH_HEAD_NO_MERGE_DATA2);
+	cl_git_pass(git_tag_delete(g_repo, "annotated_tag"));
+	cl_git_pass(git_tag_delete(g_repo, "blob"));
+	cl_git_pass(git_tag_delete(g_repo, "commit_tree"));
+	cl_git_pass(git_tag_delete(g_repo, "nearly-dangling"));
 	fetchhead_test_fetch(NULL, FETCH_HEAD_NO_MERGE_DATA);
+	cl_git_pass(git_tag_delete(g_repo, "commit_tree"));
+	fetchhead_test_fetch(NULL, FETCH_HEAD_NO_MERGE_DATA3);
 }
diff --git a/tests/pack/packbuilder.c b/tests/pack/packbuilder.c
index 1059424..228acf2 100644
--- a/tests/pack/packbuilder.c
+++ b/tests/pack/packbuilder.c
@@ -47,7 +47,7 @@ void test_pack_packbuilder__cleanup(void)
 	git_indexer_free(_indexer);
 	_indexer = NULL;
 
-	p_chdir("..");
+	cl_git_pass(p_chdir(".."));
 	cl_git_sandbox_cleanup();
 	_repo = NULL;
 }
diff --git a/tests/threads/basic.c b/tests/threads/basic.c
index a329ee7..eb15293 100644
--- a/tests/threads/basic.c
+++ b/tests/threads/basic.c
@@ -1,5 +1,6 @@
 #include "clar_libgit2.h"
 
+#include "thread_helpers.h"
 #include "cache.h"
 
 
@@ -34,3 +35,16 @@ void test_threads_basic__multiple_init(void)
 	cl_git_pass(git_repository_open(&nested_repo, cl_fixture("testrepo.git")));
 	git_repository_free(nested_repo);
 }
+
+static void *set_error(void *dummy)
+{
+	giterr_set(GITERR_INVALID, "oh no, something happened!\n");
+
+	return dummy;
+}
+
+/* Set errors so we can check that we free it */
+void test_threads_basic__set_error(void)
+{
+	run_in_parallel(1, 4, set_error, NULL, NULL);
+}