thodg/libgit2

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/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/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/pack.c b/src/pack.c
index 7c1cfe0..516e0f3 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/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/pack/packbuilder.c b/tests/pack/packbuilder.c
index 12273ec..29f3e2d 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;
 }