src/index.c

/*
 * This file is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License, version 2,
 * as published by the Free Software Foundation.
 *
 * In addition to the permissions in the GNU General Public License,
 * the authors give you unlimited permission to link the compiled
 * version of this file into combinations with other programs,
 * and to distribute those combinations without any restriction
 * coming from the use of this file.  (The General Public License
 * restrictions do apply in other respects; for example, they cover
 * modification of the file, and distribution when not linked into
 * a combined executable.)
 *
 * This file is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; see the file COPYING.  If not, write to
 * the Free Software Foundation, 51 Franklin Street, Fifth Floor,
 * Boston, MA 02110-1301, USA.
 */

#include <stddef.h>

#include "common.h"
#include "repository.h"
#include "index.h"
#include "hash.h"
#include "git2/odb.h"
#include "git2/blob.h"

#define entry_size(type,len) ((offsetof(type, path) + (len) + 8) & ~7)
#define short_entry_size(len) entry_size(struct entry_short, len)
#define long_entry_size(len) entry_size(struct entry_long, len)

#define minimal_entry_size (offsetof(struct entry_short, path))

static const size_t INDEX_FOOTER_SIZE = GIT_OID_RAWSZ;
static const size_t INDEX_HEADER_SIZE = 12;

static const unsigned int INDEX_VERSION_NUMBER = 2;
static const unsigned int INDEX_VERSION_NUMBER_EXT = 3;

static const unsigned int INDEX_HEADER_SIG = 0x44495243;
static const char INDEX_EXT_TREECACHE_SIG[] = {'T', 'R', 'E', 'E'};
static const char INDEX_EXT_UNMERGED_SIG[] = {'R', 'E', 'U', 'C'};

struct index_header {
	uint32_t signature;
	uint32_t version;
	uint32_t entry_count;
};

struct index_extension {
	char signature[4];
	uint32_t extension_size;
};

struct entry_time {
	uint32_t seconds;
	uint32_t nanoseconds;
};

struct entry_short {
	struct entry_time ctime;
	struct entry_time mtime;
	uint32_t dev;
	uint32_t ino;
	uint32_t mode;
	uint32_t uid;
	uint32_t gid;
	uint32_t file_size;
	git_oid oid;
	uint16_t flags;
	char path[1]; /* arbitrary length */
};

struct entry_long {
	struct entry_time ctime;
	struct entry_time mtime;
	uint32_t dev;
	uint32_t ino;
	uint32_t mode;
	uint32_t uid;
	uint32_t gid;
	uint32_t file_size;
	git_oid oid;
	uint16_t flags;
	uint16_t flags_extended;
	char path[1]; /* arbitrary length */
};

/* local declarations */
static size_t read_extension(git_index *index, const char *buffer, size_t buffer_size);
static size_t read_entry(git_index_entry *dest, const void *buffer, size_t buffer_size);
static int read_header(struct index_header *dest, const void *buffer);

static int read_tree(git_index *index, const char *buffer, size_t buffer_size);
static int read_tree_internal(git_index_tree **, const char **, const char *, git_index_tree *);

static int parse_index(git_index *index, const char *buffer, size_t buffer_size);
static int is_index_extended(git_index *index);
static int write_index(git_index *index, git_filebuf *file);

static int index_srch(const void *key, const void *array_member)
{
	const git_index_entry *entry = array_member;

	return strcmp(key, entry->path);
}

static int index_cmp(const void *a, const void *b)
{
	const git_index_entry *entry_a = a;
	const git_index_entry *entry_b = b;

	return strcmp(entry_a->path, entry_b->path);
}

static int unmerged_srch(const void *key, const void *array_member)
{
	const git_index_entry_unmerged *entry = array_member;

	return strcmp(key, entry->path);
}

static int unmerged_cmp(const void *a, const void *b)
{
	const git_index_entry_unmerged *info_a = a;
	const git_index_entry_unmerged *info_b = b;

	return strcmp(info_a->path, info_b->path);
}

static unsigned int index_create_mode(unsigned int mode)
{
	if (S_ISLNK(mode))
		return S_IFLNK;
	if (S_ISDIR(mode) || (mode & S_IFMT) == (S_IFLNK | S_IFDIR))
		return (S_IFLNK | S_IFDIR);
	return S_IFREG | ((mode & 0100) ? 0755 : 0644);
}

static int index_initialize(git_index **index_out, git_repository *owner, const char *index_path)
{
	git_index *index;

	assert(index_out && index_path);

	index = git__malloc(sizeof(git_index));
	if (index == NULL)
		return GIT_ENOMEM;

	memset(index, 0x0, sizeof(git_index));

	index->index_file_path = git__strdup(index_path);
	if (index->index_file_path == NULL) {
		free(index);
		return GIT_ENOMEM;
	}

	index->repository = owner;

	git_vector_init(&index->entries, 32, index_cmp);

	/* Check if index file is stored on disk already */
	if (git_futils_exists(index->index_file_path) == 0)
		index->on_disk = 1;

	*index_out = index;
	return git_index_read(index);
}

int git_index_open(git_index **index_out, const char *index_path)
{
	return index_initialize(index_out, NULL, index_path);
}

/*
 * Moved from `repository.c`
 */
int git_repository_index(git_index **index_out, git_repository *repo)
{
	if (repo->is_bare)
		return git__throw(GIT_EBAREINDEX, "Failed to open index. Repository is bare");

	return index_initialize(index_out, repo, repo->path_index);
}

void git_index_free(git_index *index)
{
	if (index == NULL)
		return;

	git_index_clear(index);
	git_vector_free(&index->entries);
	git_vector_free(&index->unmerged);

	free(index->index_file_path);
	free(index);
}

static void free_tree(git_index_tree *tree)
{
	unsigned int i;

	if (tree == NULL)
		return;

	for (i = 0; i < tree->children_count; ++i)
		free_tree(tree->children[i]);

	free(tree->name);
	free(tree->children);
	free(tree);
}

void git_index_clear(git_index *index)
{
	unsigned int i;

	assert(index);

	for (i = 0; i < index->entries.length; ++i) {
		git_index_entry *e;
		e = git_vector_get(&index->entries, i);
		free(e->path);
		free(e);
	}

	for (i = 0; i < index->unmerged.length; ++i) {
		git_index_entry_unmerged *e;
		e = git_vector_get(&index->unmerged, i);
		free(e->path);
		free(e);
	}

	git_vector_clear(&index->entries);
	git_vector_clear(&index->unmerged);
	index->last_modified = 0;

	free_tree(index->tree);
	index->tree = NULL;
}

int git_index_read(git_index *index)
{
	int error = GIT_SUCCESS, updated;
	git_fbuffer buffer = GIT_FBUFFER_INIT;
	time_t mtime;

	assert(index->index_file_path);

	if (!index->on_disk || git_futils_exists(index->index_file_path) < 0) {
		git_index_clear(index);
		index->on_disk = 0;
		return GIT_SUCCESS;
	}

	/* We don't want to update the mtime if we fail to parse the index */
	mtime = index->last_modified;
	error = git_futils_readbuffer_updated(&buffer, index->index_file_path, &mtime, &updated);
	if (error < GIT_SUCCESS)
		return git__rethrow(error, "Failed to read index");

	if (updated) {
		git_index_clear(index);
		error = parse_index(index, buffer.data, buffer.len);

		if (error == GIT_SUCCESS)
			index->last_modified = mtime;

		git_futils_freebuffer(&buffer);
	}

	if (error < GIT_SUCCESS)
		return git__rethrow(error, "Failed to parse index");
	return error;
}

int git_index_write(git_index *index)
{
	git_filebuf file;
	struct stat indexst;
	int error;

	git_vector_sort(&index->entries);

	if ((error = git_filebuf_open(&file, index->index_file_path, GIT_FILEBUF_HASH_CONTENTS)) < GIT_SUCCESS)
		return git__rethrow(error, "Failed to write index");

	if ((error = write_index(index, &file)) < GIT_SUCCESS) {
		git_filebuf_cleanup(&file);
		return git__rethrow(error, "Failed to write index");
	}

	if ((error = git_filebuf_commit(&file)) < GIT_SUCCESS)
		return git__rethrow(error, "Failed to write index");

	if (p_stat(index->index_file_path, &indexst) == 0) {
		index->last_modified = indexst.st_mtime;
		index->on_disk = 1;
	}

	return GIT_SUCCESS;
}

unsigned int git_index_entrycount(git_index *index)
{
	assert(index);
	return index->entries.length;
}

unsigned int git_index_entrycount_unmerged(git_index *index)
{
	assert(index);
	return index->unmerged.length;
}

git_index_entry *git_index_get(git_index *index, unsigned int n)
{
	git_vector_sort(&index->entries);
	return git_vector_get(&index->entries, n);
}

static int index_entry_init(git_index_entry **entry_out, git_index *index, const char *rel_path, int stage)
{
	git_index_entry *entry;
	char full_path[GIT_PATH_MAX];
	struct stat st;
	git_oid oid;
	int error;

	if (index->repository == NULL)
		return git__throw(GIT_EBAREINDEX, "Failed to initialize entry. Repository is bare");

	git_path_join(full_path, index->repository->path_workdir, rel_path);

	if (p_lstat(full_path, &st) < 0)
		return git__throw(GIT_ENOTFOUND, "Failed to initialize entry. '%s' cannot be opened", full_path);

	if (stage < 0 || stage > 3)
		return git__throw(GIT_ERROR, "Failed to initialize entry. Invalid stage %i", stage);

	/* write the blob to disk and get the oid */
	if ((error = git_blob_create_fromfile(&oid, index->repository, rel_path)) < GIT_SUCCESS)
		return git__rethrow(error, "Failed to initialize index entry");

	entry = git__malloc(sizeof(git_index_entry));
	if (!entry)
		return GIT_ENOMEM;
	memset(entry, 0x0, sizeof(git_index_entry));

	entry->ctime.seconds = (git_time_t)st.st_ctime;
	entry->mtime.seconds = (git_time_t)st.st_mtime;
	/* entry.mtime.nanoseconds = st.st_mtimensec; */
	/* entry.ctime.nanoseconds = st.st_ctimensec; */
	entry->dev= st.st_rdev;
	entry->ino = st.st_ino;
	entry->mode = index_create_mode(st.st_mode);
	entry->uid = st.st_uid;
	entry->gid = st.st_gid;
	entry->file_size = st.st_size;
	entry->oid = oid;

	entry->flags |= (stage << GIT_IDXENTRY_STAGESHIFT);
	entry->path = git__strdup(rel_path);
	if (entry->path == NULL) {
		free(entry);
		return GIT_ENOMEM;
	}

	*entry_out = entry;
	return GIT_SUCCESS;
}

static git_index_entry *index_entry_dup(const git_index_entry *source_entry)
{
	git_index_entry *entry;

	entry = git__malloc(sizeof(git_index_entry));
	if (!entry)
		return NULL;

	memcpy(entry, source_entry, sizeof(git_index_entry));

	/* duplicate the path string so we own it */
	entry->path = git__strdup(entry->path);
	if (!entry->path)
		return NULL;

	return entry;
}

static void index_entry_free(git_index_entry *entry)
{
	if (!entry)
		return;
	free(entry->path);
	free(entry);
}

static int index_insert(git_index *index, git_index_entry *entry, int replace)
{
	size_t path_length;
	int position;
	git_index_entry **entry_array;

	assert(index && entry);

	if (entry->path == NULL)
		return git__throw(GIT_EMISSINGOBJDATA, "Failed to insert into index. Entry has no path");

	/* make sure that the path length flag is correct */
	path_length = strlen(entry->path);

	entry->flags &= ~GIT_IDXENTRY_NAMEMASK;

	if (path_length < GIT_IDXENTRY_NAMEMASK)
		entry->flags |= path_length & GIT_IDXENTRY_NAMEMASK;
	else
		entry->flags |= GIT_IDXENTRY_NAMEMASK;;

	/*
	 * replacing is not requested: just insert entry at the end;
	 * the index is no longer sorted
	 */
	if (!replace) {
		if (git_vector_insert(&index->entries, entry) < GIT_SUCCESS)
			return GIT_ENOMEM;

		return GIT_SUCCESS;
	}

	/* look if an entry with this path already exists */
	position = git_index_find(index, entry->path);

	/*
	 * if no entry exists add the entry at the end;
	 * the index is no longer sorted
	 */
	if (position == GIT_ENOTFOUND) {
		if (git_vector_insert(&index->entries, entry) < GIT_SUCCESS)
			return GIT_ENOMEM;

		return GIT_SUCCESS;
	}

	/* exists, replace it */
	entry_array = (git_index_entry **) index->entries.contents;
	free(entry_array[position]->path);
	free(entry_array[position]);
	entry_array[position] = entry;

	return GIT_SUCCESS;
}

static int index_add(git_index *index, const char *path, int stage, int replace)
{
	git_index_entry *entry = NULL;
	int ret;

	ret = index_entry_init(&entry, index, path, stage);
	if (ret)
		goto err;

	ret = index_insert(index, entry, replace);
	if (ret)
		goto err;

	return ret;
err:
	index_entry_free(entry);
	return git__rethrow(ret, "Failed to append to index");
}

int git_index_add(git_index *index, const char *path, int stage)
{
	return index_add(index, path, stage, 1);
}

int git_index_append(git_index *index, const char *path, int stage)
{
	return index_add(index, path, stage, 0);
}

static int index_add2(git_index *index, const git_index_entry *source_entry,
		int replace)
{
	git_index_entry *entry = NULL;
	int ret;

	entry = index_entry_dup(source_entry);
	if (entry == NULL) {
		ret = GIT_ENOMEM;
		goto err;
	}

	ret = index_insert(index, entry, replace);
	if (ret)
		goto err;

	return ret;
err:
	index_entry_free(entry);
	return git__rethrow(ret, "Failed to append to index");
}

int git_index_add2(git_index *index, const git_index_entry *source_entry)
{
	return index_add2(index, source_entry, 1);
}

int git_index_append2(git_index *index, const git_index_entry *source_entry)
{
	return index_add2(index, source_entry, 1);
}

int git_index_remove(git_index *index, int position)
{
	git_vector_sort(&index->entries);
	return git_vector_remove(&index->entries, (unsigned int)position);
}

int git_index_find(git_index *index, const char *path)
{
	return git_vector_bsearch2(&index->entries, index_srch, path);
}

void git_index_uniq(git_index *index)
{
	git_vector_uniq(&index->entries);
}

const git_index_entry_unmerged *git_index_get_unmerged_bypath(git_index *index, const char *path)
{
	int pos;
	assert(index && path);

	if (!index->unmerged.length)
		return NULL;

	if ((pos = git_vector_bsearch2(&index->unmerged, unmerged_srch, path)) < GIT_SUCCESS)
		return NULL;

	return git_vector_get(&index->unmerged, pos);
}

const git_index_entry_unmerged *git_index_get_unmerged_byindex(git_index *index, unsigned int n)
{
	assert(index);
	return git_vector_get(&index->unmerged, n);
}


static int read_tree_internal(git_index_tree **out,
		const char **buffer_in, const char *buffer_end, git_index_tree *parent)
{
	git_index_tree *tree;
	const char *name_start, *buffer;
	long count;
	int error = GIT_SUCCESS;

	if ((tree = git__malloc(sizeof(git_index_tree))) == NULL)
		return GIT_ENOMEM;

	memset(tree, 0x0, sizeof(git_index_tree));
	tree->parent = parent;

	buffer = name_start = *buffer_in;

	if ((buffer = memchr(buffer, '\0', buffer_end - buffer)) == NULL) {
		error = GIT_EOBJCORRUPTED;
		goto cleanup;
	}

	/* NUL-terminated tree name */
	tree->name = git__strdup(name_start);
	if (tree->name == NULL) {
		error = GIT_ENOMEM;
		goto cleanup;
	}

	if (++buffer >= buffer_end) {
		error = GIT_EOBJCORRUPTED;
		goto cleanup;
	}

	/* Blank-terminated ASCII decimal number of entries in this tree */
	if (git__strtol32(&count, buffer, &buffer, 10) < GIT_SUCCESS || count < -1) {
		error = GIT_EOBJCORRUPTED;
		goto cleanup;
	}

	/* Invalidated TREE. Free the tree but report success */
	if (count == -1) {
		/* FIXME: return buffer_end or the end position for
		 * this single tree entry */
		*buffer_in = buffer_end;
		*out = NULL;
		free_tree(tree); /* Needs to be done manually */
		return GIT_SUCCESS;
	}

	tree->entries = count;

	if (*buffer != ' ' || ++buffer >= buffer_end) {
		error = GIT_EOBJCORRUPTED;
		goto cleanup;
	}

	 /* Number of children of the tree, newline-terminated */
	if (git__strtol32(&count, buffer, &buffer, 10) < GIT_SUCCESS ||
		count < 0) {
		error = GIT_EOBJCORRUPTED;
		goto cleanup;
	}

	tree->children_count = count;

	if (*buffer != '\n' || ++buffer >= buffer_end) {
		error = GIT_EOBJCORRUPTED;
		goto cleanup;
	}

	/* 160-bit SHA-1 for this tree and it's children */
	if (buffer + GIT_OID_RAWSZ > buffer_end) {
		error = GIT_EOBJCORRUPTED;
		goto cleanup;
	}

	git_oid_fromraw(&tree->oid, (const unsigned char *)buffer);
	buffer += GIT_OID_RAWSZ;

	/* Parse children: */
	if (tree->children_count > 0) {
		unsigned int i;
		int err;

		tree->children = git__malloc(tree->children_count * sizeof(git_index_tree *));
		if (tree->children == NULL)
			goto cleanup;

		for (i = 0; i < tree->children_count; ++i) {
			err = read_tree_internal(&tree->children[i], &buffer, buffer_end, tree);

			if (err < GIT_SUCCESS)
				goto cleanup;
		}
	}

	*buffer_in = buffer;
	*out = tree;
	return GIT_SUCCESS;

 cleanup:
	free_tree(tree);
	return error;
}

static int read_tree(git_index *index, const char *buffer, size_t buffer_size)
{
	const char *buffer_end = buffer + buffer_size;
	int error;

	error = read_tree_internal(&index->tree, &buffer, buffer_end, NULL);

	if (buffer < buffer_end)
		return GIT_EOBJCORRUPTED;

	return error;
}

static int read_unmerged(git_index *index, const char *buffer, size_t size)
{
	const char *endptr;
	size_t len;
	int i;

	git_vector_init(&index->unmerged, 16, unmerged_cmp);

	while (size) {
		git_index_entry_unmerged *lost;

		len = strlen(buffer) + 1;
		if (size <= len)
			return git__throw(GIT_ERROR, "Failed to read unmerged entries");

		if ((lost = git__malloc(sizeof(git_index_entry_unmerged))) == NULL)
			return GIT_ENOMEM;

		if (git_vector_insert(&index->unmerged, lost) < GIT_SUCCESS)
			return git__throw(GIT_ERROR, "Failed to read unmerged entries");

		lost->path = git__strdup(buffer);
		if (!lost->path)
			return GIT_ENOMEM;

		size -= len;
		buffer += len;

		for (i = 0; i < 3; i++) {
			long tmp;

			if (git__strtol32(&tmp, buffer, &endptr, 8) < GIT_SUCCESS ||
				!endptr || endptr == buffer || *endptr || (unsigned)tmp > UINT_MAX)
				return GIT_ERROR;

			lost->mode[i] = tmp;

			len = (endptr + 1) - buffer;
			if (size <= len)
				return git__throw(GIT_ERROR, "Failed to read unmerged entries");

			size -= len;
			buffer += len;
		}

		for (i = 0; i < 3; i++) {
			if (!lost->mode[i])
				continue;
			if (size < 20)
				return git__throw(GIT_ERROR, "Failed to read unmerged entries");
			git_oid_fromraw(&lost->oid[i], (const unsigned char *) buffer);
			size -= 20;
			buffer += 20;
		}
	}

	return GIT_SUCCESS;
}

static size_t read_entry(git_index_entry *dest, 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;

	if (INDEX_FOOTER_SIZE + minimal_entry_size > buffer_size)
		return 0;

	memset(dest, 0x0, sizeof(git_index_entry));

	dest->ctime.seconds = (git_time_t)ntohl(source->ctime.seconds);
	dest->ctime.nanoseconds = ntohl(source->ctime.nanoseconds);
	dest->mtime.seconds = (git_time_t)ntohl(source->mtime.seconds);
	dest->mtime.nanoseconds = ntohl(source->mtime.nanoseconds);
	dest->dev = ntohl(source->dev);
	dest->ino = ntohl(source->ino);
	dest->mode = ntohl(source->mode);
	dest->uid = ntohl(source->uid);
	dest->gid = ntohl(source->gid);
	dest->file_size = ntohl(source->file_size);
	git_oid_cpy(&dest->oid, &source->oid);
	dest->flags = ntohs(source->flags);

	if (dest->flags & GIT_IDXENTRY_EXTENDED) {
		const struct entry_long *source_l = (const struct entry_long *)source;
		path_ptr = source_l->path;

		flags_raw = ntohs(source_l->flags_extended);
		memcpy(&dest->flags_extended, &flags_raw, 2);
	} else
		path_ptr = source->path;

	path_length = dest->flags & GIT_IDXENTRY_NAMEMASK;

	/* if this is a very long string, we must find its
	 * real length without overflowing */
	if (path_length == 0xFFF) {
		const char *path_end;

		path_end = memchr(path_ptr, '\0', buffer_size);
		if (path_end == NULL)
				return 0;

		path_length = path_end - path_ptr;
	}

	if (dest->flags & GIT_IDXENTRY_EXTENDED)
		entry_size = long_entry_size(path_length);
	else
		entry_size = short_entry_size(path_length);

	if (INDEX_FOOTER_SIZE + entry_size > buffer_size)
		return 0;

	dest->path = git__strdup(path_ptr);
	assert(dest->path);

	return entry_size;
}

static int read_header(struct index_header *dest, const void *buffer)
{
	const struct index_header *source = buffer;

	dest->signature = ntohl(source->signature);
	if (dest->signature != INDEX_HEADER_SIG)
		return GIT_EOBJCORRUPTED;

	dest->version = ntohl(source->version);
	if (dest->version != INDEX_VERSION_NUMBER_EXT &&
		dest->version != INDEX_VERSION_NUMBER)
		return GIT_EOBJCORRUPTED;

	dest->entry_count = ntohl(source->entry_count);
	return GIT_SUCCESS;
}

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);

	total_size = dest.extension_size + sizeof(struct index_extension);

	if (buffer_size - total_size < INDEX_FOOTER_SIZE)
		return 0;

	/* optional extension */
	if (dest.signature[0] >= 'A' && dest.signature[0] <= 'Z') {
		/* tree cache */
		if (memcmp(dest.signature, INDEX_EXT_TREECACHE_SIG, 4) == 0) {
			if (read_tree(index, buffer + 8, dest.extension_size) < GIT_SUCCESS)
				return 0;
		} else if (memcmp(dest.signature, INDEX_EXT_UNMERGED_SIG, 4) == 0) {
			if (read_unmerged(index, buffer + 8, dest.extension_size) < GIT_SUCCESS)
				return 0;
		}
		/* else, unsupported extension. We cannot parse this, but we can skip
		 * it by returning `total_size */
	} else {
		/* we cannot handle non-ignorable extensions;
		 * in fact they aren't even defined in the standard */
		return 0;
	}

	return total_size;
}

static int parse_index(git_index *index, const char *buffer, size_t buffer_size)
{
	unsigned int i;
	struct index_header header;
	git_oid checksum_calculated, checksum_expected;

#define seek_forward(_increase) { \
	if (_increase >= buffer_size) \
		return git__throw(GIT_EOBJCORRUPTED, "Failed to seek forward. Buffer size exceeded"); \
	buffer += _increase; \
	buffer_size -= _increase;\
}

	if (buffer_size < INDEX_HEADER_SIZE + INDEX_FOOTER_SIZE)
		return git__throw(GIT_EOBJCORRUPTED, "Failed to parse index. Buffer too small");

	/* Precalculate the SHA1 of the files's contents -- we'll match it to
	 * the provided SHA1 in the footer */
	git_hash_buf(&checksum_calculated, buffer, buffer_size - INDEX_FOOTER_SIZE);

	/* Parse header */
	if (read_header(&header, buffer) < GIT_SUCCESS)
		return git__throw(GIT_EOBJCORRUPTED, "Failed to parse index. Header is corrupted");

	seek_forward(INDEX_HEADER_SIZE);

	git_vector_clear(&index->entries);

	/* Parse all the entries */
	for (i = 0; i < header.entry_count && buffer_size > INDEX_FOOTER_SIZE; ++i) {
		size_t entry_size;
		git_index_entry *entry;

		entry = git__malloc(sizeof(git_index_entry));
		if (entry == NULL)
			return GIT_ENOMEM;

		entry_size = read_entry(entry, buffer, buffer_size);

		/* 0 bytes read means an object corruption */
		if (entry_size == 0)
			return git__throw(GIT_EOBJCORRUPTED, "Failed to parse index. Entry size is zero");

		if (git_vector_insert(&index->entries, entry) < GIT_SUCCESS)
			return GIT_ENOMEM;

		seek_forward(entry_size);
	}

	if (i != header.entry_count)
		return git__throw(GIT_EOBJCORRUPTED, "Failed to parse index. Header entries changed while parsing");

	/* There's still space for some extensions! */
	while (buffer_size > INDEX_FOOTER_SIZE) {
		size_t extension_size;

		extension_size = read_extension(index, buffer, buffer_size);

		/* see if we have read any bytes from the extension */
		if (extension_size == 0)
			return git__throw(GIT_EOBJCORRUPTED, "Failed to parse index. Extension size is zero");

		seek_forward(extension_size);
	}

	if (buffer_size != INDEX_FOOTER_SIZE)
		return git__throw(GIT_EOBJCORRUPTED, "Failed to parse index. Buffer size does not match index footer size");

	/* 160-bit SHA-1 over the content of the index file before this checksum. */
	git_oid_fromraw(&checksum_expected, (const unsigned char *)buffer);

	if (git_oid_cmp(&checksum_calculated, &checksum_expected) != 0)
		return git__throw(GIT_EOBJCORRUPTED, "Failed to parse index. Calculated checksum does not match expected checksum");

#undef seek_forward

	/* force sorting in the vector: the entries are
	 * assured to be sorted on the index */
	index->entries.sorted = 1;
	return GIT_SUCCESS;
}

static int is_index_extended(git_index *index)
{
	unsigned int i, extended;

	extended = 0;

	for (i = 0; i < index->entries.length; ++i) {
		git_index_entry *entry;
		entry = git_vector_get(&index->entries, i);
		entry->flags &= ~GIT_IDXENTRY_EXTENDED;
		if (entry->flags_extended & GIT_IDXENTRY_EXTENDED_FLAGS) {
			extended++;
			entry->flags |= GIT_IDXENTRY_EXTENDED;
		}
	}
	return extended;
}

static int write_disk_entry(git_filebuf *file, git_index_entry *entry)
{
	struct entry_short *ondisk;
	size_t path_len, disk_size;
	char *path;

	path_len = strlen(entry->path);

	if (entry->flags & GIT_IDXENTRY_EXTENDED)
		disk_size = long_entry_size(path_len);
	else
		disk_size = short_entry_size(path_len);

	if (git_filebuf_reserve(file, (void **)&ondisk, disk_size) < GIT_SUCCESS)
		return GIT_ENOMEM;

	memset(ondisk, 0x0, disk_size);

	/**
	 * Yes, we have to truncate.
	 *
	 * The on-disk format for Index entries clearly defines
	 * the time and size fields to be 4 bytes each -- so even if
	 * we store these values with 8 bytes on-memory, they must
	 * be truncated to 4 bytes before writing to disk.
	 *
	 * In 2038 I will be either too dead or too rich to care about this
	 */
	ondisk->ctime.seconds = htonl((uint32_t)entry->ctime.seconds);
	ondisk->mtime.seconds = htonl((uint32_t)entry->mtime.seconds);
	ondisk->ctime.nanoseconds = htonl(entry->ctime.nanoseconds);
	ondisk->mtime.nanoseconds = htonl(entry->mtime.nanoseconds);
	ondisk->dev  = htonl(entry->dev);
	ondisk->ino  = htonl(entry->ino);
	ondisk->mode = htonl(entry->mode);
	ondisk->uid  = htonl(entry->uid);
	ondisk->gid  = htonl(entry->gid);
	ondisk->file_size = htonl((uint32_t)entry->file_size);

	git_oid_cpy(&ondisk->oid, &entry->oid);

	ondisk->flags = htons(entry->flags);

	if (entry->flags & GIT_IDXENTRY_EXTENDED) {
		struct entry_long *ondisk_ext;
		ondisk_ext = (struct entry_long *)ondisk;
		ondisk_ext->flags_extended = htons(entry->flags_extended);
		path = ondisk_ext->path;
	}
	else
		path = ondisk->path;

	memcpy(path, entry->path, path_len);

	return GIT_SUCCESS;
}

static int write_entries(git_index *index, git_filebuf *file)
{
	unsigned int i;

	for (i = 0; i < index->entries.length; ++i) {
		git_index_entry *entry;
		entry = git_vector_get(&index->entries, i);
		if (write_disk_entry(file, entry) < GIT_SUCCESS)
			return GIT_ENOMEM;
	}

	return GIT_SUCCESS;
}

static int write_index(git_index *index, git_filebuf *file)
{
	int error = GIT_SUCCESS;
	git_oid hash_final;

	struct index_header header;

	int is_extended;

	assert(index && file);

	is_extended = is_index_extended(index);

	header.signature = htonl(INDEX_HEADER_SIG);
	header.version = htonl(is_extended ? INDEX_VERSION_NUMBER_EXT : INDEX_VERSION_NUMBER);
	header.entry_count = htonl(index->entries.length);

	git_filebuf_write(file, &header, sizeof(struct index_header));

	error = write_entries(index, file);
	if (error < GIT_SUCCESS)
		return git__rethrow(error, "Failed to write index");

	/* TODO: write extensions (tree cache) */

	/* get out the hash for all the contents we've appended to the file */
	git_filebuf_hash(&hash_final, file);

	/* write it at the end of the file */
	git_filebuf_write(file, hash_final.id, GIT_OID_RAWSZ);

	return error == GIT_SUCCESS ? GIT_SUCCESS : git__rethrow(error, "Failed to write index");
}

int git_index_entry_stage(const git_index_entry *entry)
{
	return (entry->flags & GIT_IDXENTRY_STAGEMASK) >> GIT_IDXENTRY_STAGESHIFT;
}