text: /*
   * Copyright (C) the libgit2 contributors. All rights reserved.
   *
   * This file is part of libgit2, distributed under the GNU GPL v2 with
   * a Linking Exception. For full terms see the included COPYING file.
   */
  
  #include <stddef.h>
  
  #include "common.h"
  #include "repository.h"
  #include "index.h"
  #include "tree.h"
  #include "tree-cache.h"
  #include "hash.h"
  #include "iterator.h"
  #include "pathspec.h"
  #include "ignore.h"
  
  #include "git2/odb.h"
  #include "git2/oid.h"
  #include "git2/blob.h"
  #include "git2/config.h"
  #include "git2/sys/index.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'};
  static const char INDEX_EXT_CONFLICT_NAME_SIG[] = {'N', 'A', 'M', 'E'};
  
  #define INDEX_OWNER(idx) ((git_repository *)(GIT_REFCOUNT_OWNER(idx)))
  
  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 */
  };
  
  struct entry_srch_key {
  	const char *path;
  	int stage;
  };
  
  /* 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 parse_index(git_index *index, const char *buffer, size_t buffer_size);
  static bool is_index_extended(git_index *index);
  static int write_index(git_index *index, git_filebuf *file);
  
  static void index_entry_free(git_index_entry *entry);
  static void index_entry_reuc_free(git_index_reuc_entry *reuc);
  
  static int index_srch(const void *key, const void *array_member)
  {
  	const struct entry_srch_key *srch_key = key;
  	const git_index_entry *entry = array_member;
  	int ret;
  
  	ret = strcmp(srch_key->path, entry->path);
  
  	if (ret == 0 && srch_key->stage != GIT_INDEX_STAGE_ANY)
  		ret = srch_key->stage - GIT_IDXENTRY_STAGE(entry);
  
  	return ret;
  }
  
  static int index_isrch(const void *key, const void *array_member)
  {
  	const struct entry_srch_key *srch_key = key;
  	const git_index_entry *entry = array_member;
  	int ret;
  
  	ret = strcasecmp(srch_key->path, entry->path);
  
  	if (ret == 0 && srch_key->stage != GIT_INDEX_STAGE_ANY)
  		ret = srch_key->stage - GIT_IDXENTRY_STAGE(entry);
  
  	return ret;
  }
  
  static int index_cmp_path(const void *a, const void *b)
  {
  	return strcmp((const char *)a, (const char *)b);
  }
  
  static int index_icmp_path(const void *a, const void *b)
  {
  	return strcasecmp((const char *)a, (const char *)b);
  }
  
  static int index_srch_path(const void *path, const void *array_member)
  {
  	const git_index_entry *entry = array_member;
  
  	return strcmp((const char *)path, entry->path);
  }
  
  static int index_isrch_path(const void *path, const void *array_member)
  {
  	const git_index_entry *entry = array_member;
  
  	return strcasecmp((const char *)path, entry->path);
  }
  
  static int index_cmp(const void *a, const void *b)
  {
  	int diff;
  	const git_index_entry *entry_a = a;
  	const git_index_entry *entry_b = b;
  
  	diff = strcmp(entry_a->path, entry_b->path);
  
  	if (diff == 0)
  		diff = (GIT_IDXENTRY_STAGE(entry_a) - GIT_IDXENTRY_STAGE(entry_b));
  
  	return diff;
  }
  
  static int index_icmp(const void *a, const void *b)
  {
  	int diff;
  	const git_index_entry *entry_a = a;
  	const git_index_entry *entry_b = b;
  
  	diff = strcasecmp(entry_a->path, entry_b->path);
  
  	if (diff == 0)
  		diff = (GIT_IDXENTRY_STAGE(entry_a) - GIT_IDXENTRY_STAGE(entry_b));
  
  	return diff;
  }
  
  static int conflict_name_cmp(const void *a, const void *b)
  {
  	const git_index_name_entry *name_a = a;
  	const git_index_name_entry *name_b = b;
  
  	if (name_a->ancestor && !name_b->ancestor)
  		return 1;
  
  	if (!name_a->ancestor && name_b->ancestor)
  		return -1;
  
  	if (name_a->ancestor)
  		return strcmp(name_a->ancestor, name_b->ancestor);
  
  	if (!name_a->ours || !name_b->ours)
  		return 0;
  
  	return strcmp(name_a->ours, name_b->ours);
  }
  
  /**
   * TODO: enable this when resolving case insensitive conflicts
   */
  #if 0
  static int conflict_name_icmp(const void *a, const void *b)
  {
  	const git_index_name_entry *name_a = a;
  	const git_index_name_entry *name_b = b;
  
  	if (name_a->ancestor && !name_b->ancestor)
  		return 1;
  
  	if (!name_a->ancestor && name_b->ancestor)
  		return -1;
  
  	if (name_a->ancestor)
  		return strcasecmp(name_a->ancestor, name_b->ancestor);
  
  	if (!name_a->ours || !name_b->ours)
  		return 0;
  
  	return strcasecmp(name_a->ours, name_b->ours);
  }
  #endif
  
  static int reuc_srch(const void *key, const void *array_member)
  {
  	const git_index_reuc_entry *reuc = array_member;
  
  	return strcmp(key, reuc->path);
  }
  
  static int reuc_isrch(const void *key, const void *array_member)
  {
  	const git_index_reuc_entry *reuc = array_member;
  
  	return strcasecmp(key, reuc->path);
  }
  
  static int reuc_cmp(const void *a, const void *b)
  {
  	const git_index_reuc_entry *info_a = a;
  	const git_index_reuc_entry *info_b = b;
  
  	return strcmp(info_a->path, info_b->path);
  }
  
  static int reuc_icmp(const void *a, const void *b)
  {
  	const git_index_reuc_entry *info_a = a;
  	const git_index_reuc_entry *info_b = b;
  
  	return strcasecmp(info_a->path, info_b->path);
  }
  
  static void index_entry_reuc_free(git_index_reuc_entry *reuc)
  {
  	if (!reuc)
  		return;
  	git__free(reuc->path);
  	git__free(reuc);
  }
  
  static void index_entry_free(git_index_entry *entry)
  {
  	if (!entry)
  		return;
  	git__free(entry->path);
  	git__free(entry);
  }
  
  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 unsigned int index_merge_mode(
  	git_index *index, git_index_entry *existing, unsigned int mode)
  {
  	if (index->no_symlinks && S_ISREG(mode) &&
  		existing && S_ISLNK(existing->mode))
  		return existing->mode;
  
  	if (index->distrust_filemode && S_ISREG(mode))
  		return (existing && S_ISREG(existing->mode)) ?
  			existing->mode : index_create_mode(0666);
  
  	return index_create_mode(mode);
  }
  
  void git_index__set_ignore_case(git_index *index, bool ignore_case)
  {
  	index->ignore_case = ignore_case;
  
  	index->entries_cmp_path = ignore_case ? index_icmp_path : index_cmp_path;
  	index->entries_search = ignore_case ? index_isrch : index_srch;
  	index->entries_search_path = ignore_case ? index_isrch_path : index_srch_path;
  
  	git_vector_set_cmp(&index->entries, ignore_case ? index_icmp : index_cmp);
  	git_vector_sort(&index->entries);
  
  	index->reuc_search = ignore_case ? reuc_isrch : reuc_srch;
  
  	git_vector_set_cmp(&index->reuc, ignore_case ? reuc_icmp : reuc_cmp);
  	git_vector_sort(&index->reuc);
  }
  
  int git_index_open(git_index **index_out, const char *index_path)
  {
  	git_index *index;
  
  	assert(index_out);
  
  	index = git__calloc(1, sizeof(git_index));
  	GITERR_CHECK_ALLOC(index);
  
  	if (index_path != NULL) {
  		index->index_file_path = git__strdup(index_path);
  		GITERR_CHECK_ALLOC(index->index_file_path);
  
  		/* Check if index file is stored on disk already */
  		if (git_path_exists(index->index_file_path) == true)
  			index->on_disk = 1;
  	}
  
  	if (git_vector_init(&index->entries, 32, index_cmp) < 0 ||
  		git_vector_init(&index->names, 32, conflict_name_cmp) < 0 ||
  		git_vector_init(&index->reuc, 32, reuc_cmp) < 0)
  		return -1;
  
  	index->entries_cmp_path = index_cmp_path;
  	index->entries_search = index_srch;
  	index->entries_search_path = index_srch_path;
  	index->reuc_search = reuc_srch;
  
  	*index_out = index;
  	GIT_REFCOUNT_INC(index);
  
  	return (index_path != NULL) ? git_index_read(index) : 0;
  }
  
  int git_index_new(git_index **out)
  {
  	return git_index_open(out, NULL);
  }
  
  static void index_free(git_index *index)
  {
  	git_index_clear(index);
  	git_vector_free(&index->entries);
  	git_vector_free(&index->names);
  	git_vector_free(&index->reuc);
  
  	git__free(index->index_file_path);
  
  	git__memzero(index, sizeof(*index));
  	git__free(index);
  }
  
  void git_index_free(git_index *index)
  {
  	if (index == NULL)
  		return;
  
  	GIT_REFCOUNT_DEC(index, index_free);
  }
  
  static void index_entries_free(git_vector *entries)
  {
  	size_t i;
  
  	for (i = 0; i < entries->length; ++i)
  		index_entry_free(git__swap(entries->contents[i], NULL));
  
  	git_vector_clear(entries);
  }
  
  void git_index_clear(git_index *index)
  {
  	assert(index);
  
  	index_entries_free(&index->entries);
  	git_index_reuc_clear(index);
  	git_index_name_clear(index);
  
  	git_futils_filestamp_set(&index->stamp, NULL);
  
  	git_tree_cache_free(index->tree);
  	index->tree = NULL;
  }
  
  static int create_index_error(int error, const char *msg)
  {
  	giterr_set(GITERR_INDEX, msg);
  	return error;
  }
  
  int git_index_set_caps(git_index *index, unsigned int caps)
  {
  	int old_ignore_case;
  
  	assert(index);
  
  	old_ignore_case = index->ignore_case;
  
  	if (caps == GIT_INDEXCAP_FROM_OWNER) {
  		git_repository *repo = INDEX_OWNER(index);
  		int val;
  
  		if (!repo)
  			return create_index_error(
  				-1, "Cannot access repository to set index caps");
  
  		if (!git_repository__cvar(&val, repo, GIT_CVAR_IGNORECASE))
  			index->ignore_case = (val != 0);
  		if (!git_repository__cvar(&val, repo, GIT_CVAR_FILEMODE))
  			index->distrust_filemode = (val == 0);
  		if (!git_repository__cvar(&val, repo, GIT_CVAR_SYMLINKS))
  			index->no_symlinks = (val == 0);
  	}
  	else {
  		index->ignore_case = ((caps & GIT_INDEXCAP_IGNORE_CASE) != 0);
  		index->distrust_filemode = ((caps & GIT_INDEXCAP_NO_FILEMODE) != 0);
  		index->no_symlinks = ((caps & GIT_INDEXCAP_NO_SYMLINKS) != 0);
  	}
  
  	if (old_ignore_case != index->ignore_case) {
  		git_index__set_ignore_case(index, index->ignore_case);
  	}
  
  	return 0;
  }
  
  unsigned int git_index_caps(const git_index *index)
  {
  	return ((index->ignore_case ? GIT_INDEXCAP_IGNORE_CASE : 0) |
  			(index->distrust_filemode ? GIT_INDEXCAP_NO_FILEMODE : 0) |
  			(index->no_symlinks ? GIT_INDEXCAP_NO_SYMLINKS : 0));
  }
  
  int git_index_read(git_index *index)
  {
  	int error = 0, updated;
  	git_buf buffer = GIT_BUF_INIT;
  	git_futils_filestamp stamp = {0};
  
  	if (!index->index_file_path)
  		return create_index_error(-1,
  			"Failed to read index: The index is in-memory only");
  
  	if (!index->on_disk || git_path_exists(index->index_file_path) == false) {
  		git_index_clear(index);
  		index->on_disk = 0;
  		return 0;
  	}
  
  	updated = git_futils_filestamp_check(&stamp, index->index_file_path);
  	if (updated <= 0)
  		return updated;
  
  	error = git_futils_readbuffer(&buffer, index->index_file_path);
  	if (error < 0)
  		return error;
  
  	git_index_clear(index);
  	error = parse_index(index, buffer.ptr, buffer.size);
  
  	if (!error)
  		git_futils_filestamp_set(&index->stamp, &stamp);
  
  	git_buf_free(&buffer);
  	return error;
  }
  
  int git_index_write(git_index *index)
  {
  	git_filebuf file = GIT_FILEBUF_INIT;
  	int error;
  
  	if (!index->index_file_path)
  		return create_index_error(-1,
  			"Failed to read index: The index is in-memory only");
  
  	git_vector_sort(&index->entries);
  	git_vector_sort(&index->reuc);
  
  	if ((error = git_filebuf_open(
  			 &file, index->index_file_path, GIT_FILEBUF_HASH_CONTENTS)) < 0)
  		return error;
  
  	if ((error = write_index(index, &file)) < 0) {
  		git_filebuf_cleanup(&file);
  		return error;
  	}
  
  	if ((error = git_filebuf_commit(&file, GIT_INDEX_FILE_MODE)) < 0)
  		return error;
  
  	error = git_futils_filestamp_check(&index->stamp, index->index_file_path);
  	if (error < 0)
  		return error;
  
  	index->on_disk = 1;
  	return 0;
  }
  
  const char * git_index_path(git_index *index)
  {
  	assert(index);
  	return index->index_file_path;
  }
  
  int git_index_write_tree(git_oid *oid, git_index *index)
  {
  	git_repository *repo;
  
  	assert(oid && index);
  
  	repo = INDEX_OWNER(index);
  
  	if (repo == NULL)
  		return create_index_error(-1, "Failed to write tree. "
  		  "The index file is not backed up by an existing repository");
  
  	return git_tree__write_index(oid, index, repo);
  }
  
  int git_index_write_tree_to(git_oid *oid, git_index *index, git_repository *repo)
  {
  	assert(oid && index && repo);
  	return git_tree__write_index(oid, index, repo);
  }
  
  size_t git_index_entrycount(const git_index *index)
  {
  	assert(index);
  	return index->entries.length;
  }
  
  const git_index_entry *git_index_get_byindex(
  	git_index *index, size_t n)
  {
  	assert(index);
  	git_vector_sort(&index->entries);
  	return git_vector_get(&index->entries, n);
  }
  
  const git_index_entry *git_index_get_bypath(
  	git_index *index, const char *path, int stage)
  {
  	size_t pos;
  
  	assert(index);
  
  	git_vector_sort(&index->entries);
  
  	if (git_index__find(&pos, index, path, stage) < 0) {
  		giterr_set(GITERR_INDEX, "Index does not contain %s", path);
  		return NULL;
  	}
  
  	return git_index_get_byindex(index, pos);
  }
  
  void git_index_entry__init_from_stat(git_index_entry *entry, struct stat *st)
  {
  	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;
  }
  
  int git_index_entry__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);
  }
  
  int git_index_entry__cmp_icase(const void *a, const void *b)
  {
  	const git_index_entry *entry_a = a;
  	const git_index_entry *entry_b = b;
  
  	return strcasecmp(entry_a->path, entry_b->path);
  }
  
  static int index_entry_init(git_index_entry **entry_out, git_index *index, const char *rel_path)
  {
  	git_index_entry *entry = NULL;
  	struct stat st;
  	git_oid oid;
  	const char *workdir;
  	git_buf full_path = GIT_BUF_INIT;
  	int error;
  
  	if (INDEX_OWNER(index) == NULL)
  		return create_index_error(-1,
  			"Could not initialize index entry. "
  			"Index is not backed up by an existing repository.");
  
  	workdir = git_repository_workdir(INDEX_OWNER(index));
  
  	if (!workdir)
  		return create_index_error(GIT_EBAREREPO,
  			"Could not initialize index entry. Repository is bare");
  
  	if ((error = git_buf_joinpath(&full_path, workdir, rel_path)) < 0)
  		return error;
  
  	if ((error = git_path_lstat(full_path.ptr, &st)) < 0) {
  		git_buf_free(&full_path);
  		return error;
  	}
  
  	git_buf_free(&full_path); /* done with full path */
  
  	/* There is no need to validate the rel_path here, since it will be
  	 * immediately validated by the call to git_blob_create_fromfile.
  	 */
  
  	/* write the blob to disk and get the oid */
  	if ((error = git_blob_create_fromworkdir(&oid, INDEX_OWNER(index), rel_path)) < 0)
  		return error;
  
  	entry = git__calloc(1, sizeof(git_index_entry));
  	GITERR_CHECK_ALLOC(entry);
  
  	git_index_entry__init_from_stat(entry, &st);
  
  	entry->oid = oid;
  	entry->path = git__strdup(rel_path);
  	GITERR_CHECK_ALLOC(entry->path);
  
  	*entry_out = entry;
  	return 0;
  }
  
  static int index_entry_reuc_init(git_index_reuc_entry **reuc_out,
  	const char *path,
  	int ancestor_mode, const git_oid *ancestor_oid,
  	int our_mode, const git_oid *our_oid,
  	int their_mode, const git_oid *their_oid)
  {
  	git_index_reuc_entry *reuc = NULL;
  
  	assert(reuc_out && path);
  
  	*reuc_out = NULL;
  
  	reuc = git__calloc(1, sizeof(git_index_reuc_entry));
  	GITERR_CHECK_ALLOC(reuc);
  
  	reuc->path = git__strdup(path);
  	if (reuc->path == NULL)
  		return -1;
  
  	if ((reuc->mode[0] = ancestor_mode) > 0)
  		git_oid_cpy(&reuc->oid[0], ancestor_oid);
  
  	if ((reuc->mode[1] = our_mode) > 0)
  		git_oid_cpy(&reuc->oid[1], our_oid);
  
  	if ((reuc->mode[2] = their_mode) > 0)
  		git_oid_cpy(&reuc->oid[2], their_oid);
  
  	*reuc_out = reuc;
  	return 0;
  }
  
  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 int index_insert(git_index *index, git_index_entry *entry, int replace)
  {
  	size_t path_length, position;
  	git_index_entry **existing = NULL;
  
  	assert(index && entry && entry->path != NULL);
  
  	/* 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;
  
  	/* look if an entry with this path already exists */
  	if (!git_index__find(
  			&position, index, entry->path, GIT_IDXENTRY_STAGE(entry))) {
  		existing = (git_index_entry **)&index->entries.contents[position];
  
  		/* update filemode to existing values if stat is not trusted */
  		entry->mode = index_merge_mode(index, *existing, entry->mode);
  	}
  
  	/* if replacing is not requested or no existing entry exists, just
  	 * insert entry at the end; the index is no longer sorted
  	 */
  	if (!replace || !existing)
  		return git_vector_insert(&index->entries, entry);
  
  	/* exists, replace it (preserving name from existing entry) */
  	git__free(entry->path);
  	entry->path = (*existing)->path;
  	git__free(*existing);
  	*existing = entry;
  
  	return 0;
  }
  
  static int index_conflict_to_reuc(git_index *index, const char *path)
  {
  	const git_index_entry *conflict_entries[3];
  	int ancestor_mode, our_mode, their_mode;
  	git_oid const *ancestor_oid, *our_oid, *their_oid;
  	int ret;
  
  	if ((ret = git_index_conflict_get(&conflict_entries[0],
  		&conflict_entries[1], &conflict_entries[2], index, path)) < 0)
  		return ret;
  
  	ancestor_mode = conflict_entries[0] == NULL ? 0 : conflict_entries[0]->mode;
  	our_mode = conflict_entries[1] == NULL ? 0 : conflict_entries[1]->mode;
  	their_mode = conflict_entries[2] == NULL ? 0 : conflict_entries[2]->mode;
  
  	ancestor_oid = conflict_entries[0] == NULL ? NULL : &conflict_entries[0]->oid;
  	our_oid = conflict_entries[1] == NULL ? NULL : &conflict_entries[1]->oid;
  	their_oid = conflict_entries[2] == NULL ? NULL : &conflict_entries[2]->oid;
  
  	if ((ret = git_index_reuc_add(index, path, ancestor_mode, ancestor_oid,
  		our_mode, our_oid, their_mode, their_oid)) >= 0)
  		ret = git_index_conflict_remove(index, path);
  
  	return ret;
  }
  
  int git_index_add_bypath(git_index *index, const char *path)
  {
  	git_index_entry *entry = NULL;
  	int ret;
  
  	assert(index && path);
  
  	if ((ret = index_entry_init(&entry, index, path)) < 0 ||
  		(ret = index_insert(index, entry, 1)) < 0)
  		goto on_error;
  
  	/* Adding implies conflict was resolved, move conflict entries to REUC */
  	if ((ret = index_conflict_to_reuc(index, path)) < 0 && ret != GIT_ENOTFOUND)
  		goto on_error;
  
  	git_tree_cache_invalidate_path(index->tree, entry->path);
  	return 0;
  
  on_error:
  	index_entry_free(entry);
  	return ret;
  }
  
  int git_index_remove_bypath(git_index *index, const char *path)
  {
  	int ret;
  
  	assert(index && path);
  
  	if (((ret = git_index_remove(index, path, 0)) < 0 &&
  		ret != GIT_ENOTFOUND) ||
  		((ret = index_conflict_to_reuc(index, path)) < 0 &&
  		ret != GIT_ENOTFOUND))
  		return ret;
  
  	return 0;
  }
  
  int git_index_add(git_index *index, const git_index_entry *source_entry)
  {
  	git_index_entry *entry = NULL;
  	int ret;
  
  	entry = index_entry_dup(source_entry);
  	if (entry == NULL)
  		return -1;
  
  	if ((ret = index_insert(index, entry, 1)) < 0) {
  		index_entry_free(entry);
  		return ret;
  	}
  
  	git_tree_cache_invalidate_path(index->tree, entry->path);
  	return 0;
  }
  
  int git_index_remove(git_index *index, const char *path, int stage)
  {
  	size_t position;
  	int error;
  	git_index_entry *entry;
  
  	git_vector_sort(&index->entries);
  
  	if (git_index__find(&position, index, path, stage) < 0) {
  		giterr_set(GITERR_INDEX, "Index does not contain %s at stage %d",
  			path, stage);
  		return GIT_ENOTFOUND;
  	}
  
  	entry = git_vector_get(&index->entries, position);
  	if (entry != NULL)
  		git_tree_cache_invalidate_path(index->tree, entry->path);
  
  	error = git_vector_remove(&index->entries, position);
  
  	if (!error)
  		index_entry_free(entry);
  
  	return error;
  }
  
  int git_index_remove_directory(git_index *index, const char *dir, int stage)
  {
  	git_buf pfx = GIT_BUF_INIT;
  	int error = 0;
  	size_t pos;
  	git_index_entry *entry;
  
  	if (git_buf_sets(&pfx, dir) < 0 || git_path_to_dir(&pfx) < 0)
  		return -1;
  
  	git_vector_sort(&index->entries);
  
  	pos = git_index__prefix_position(index, pfx.ptr);
  
  	while (1) {
  		entry = git_vector_get(&index->entries, pos);
  		if (!entry || git__prefixcmp(entry->path, pfx.ptr) != 0)
  			break;
  
  		if (GIT_IDXENTRY_STAGE(entry) != stage) {
  			++pos;
  			continue;
  		}
  
  		git_tree_cache_invalidate_path(index->tree, entry->path);
  
  		if ((error = git_vector_remove(&index->entries, pos)) < 0)
  			break;
  		index_entry_free(entry);
  
  		/* removed entry at 'pos' so we don't need to increment it */
  	}
  
  	git_buf_free(&pfx);
  
  	return error;
  }
  
  int git_index__find(
  	size_t *at_pos, git_index *index, const char *path, int stage)
  {
  	struct entry_srch_key srch_key;
  
  	assert(path);
  
  	srch_key.path = path;
  	srch_key.stage = stage;
  
  	return git_vector_bsearch2(
  		at_pos, &index->entries, index->entries_search, &srch_key);
  }
  
  int git_index_find(size_t *at_pos, git_index *index, const char *path)
  {
  	size_t pos;
  
  	assert(index && path);
  
  	if (git_vector_bsearch2(&pos, &index->entries, index->entries_search_path, path) < 0) {
  		giterr_set(GITERR_INDEX, "Index does not contain %s", path);
  		return GIT_ENOTFOUND;
  	}
  
  	/* Since our binary search only looked at path, we may be in the
  	 * middle of a list of stages.
  	 */
  	while (pos > 0) {
  		const git_index_entry *prev = git_vector_get(&index->entries, pos-1);
  
  		if (index->entries_cmp_path(prev->path, path) != 0)
  			break;
  
  		--pos;
  	}
  
  	if (at_pos)
  		*at_pos = pos;
  
  	return 0;
  }
  
  size_t git_index__prefix_position(git_index *index, const char *path)
  {
  	struct entry_srch_key srch_key;
  	size_t pos;
  
  	srch_key.path = path;
  	srch_key.stage = 0;
  
  	git_vector_sort(&index->entries);
  	git_vector_bsearch2(
  		&pos, &index->entries, index->entries_search, &srch_key);
  
  	return pos;
  }
  
  int git_index_conflict_add(git_index *index,
  	const git_index_entry *ancestor_entry,
  	const git_index_entry *our_entry,
  	const git_index_entry *their_entry)
  {
  	git_index_entry *entries[3] = { 0 };
  	unsigned short i;
  	int ret = 0;
  
  	assert (index);
  
  	if ((ancestor_entry != NULL && (entries[0] = index_entry_dup(ancestor_entry)) == NULL) ||
  		(our_entry != NULL && (entries[1] = index_entry_dup(our_entry)) == NULL) ||
  		(their_entry != NULL && (entries[2] = index_entry_dup(their_entry)) == NULL))
  		return -1;
  
  	for (i = 0; i < 3; i++) {
  		if (entries[i] == NULL)
  			continue;
  
  		/* Make sure stage is correct */
  		entries[i]->flags = (entries[i]->flags & ~GIT_IDXENTRY_STAGEMASK) |
  			((i+1) << GIT_IDXENTRY_STAGESHIFT);
  
  		if ((ret = index_insert(index, entries[i], 1)) < 0)
  			goto on_error;
  	}
  
  	return 0;
  
  on_error:
  	for (i = 0; i < 3; i++) {
  		if (entries[i] != NULL)
  			index_entry_free(entries[i]);
  	}
  
  	return ret;
  }
  
  static int index_conflict__get_byindex(
  	const git_index_entry **ancestor_out,
  	const git_index_entry **our_out,
  	const git_index_entry **their_out,
  	git_index *index,
  	size_t n)
  {
  	const git_index_entry *conflict_entry;
  	const char *path = NULL;
  	size_t count;
  	int stage, len = 0;
  
  	assert(ancestor_out && our_out && their_out && index);
  
  	*ancestor_out = NULL;
  	*our_out = NULL;
  	*their_out = NULL;
  
  	for (count = git_index_entrycount(index); n < count; ++n) {
  		conflict_entry = git_vector_get(&index->entries, n);
  
  		if (path && index->entries_cmp_path(conflict_entry->path, path) != 0)
  			break;
  
  		stage = GIT_IDXENTRY_STAGE(conflict_entry);
  		path = conflict_entry->path;
  
  		switch (stage) {
  		case 3:
  			*their_out = conflict_entry;
  			len++;
  			break;
  		case 2:
  			*our_out = conflict_entry;
  			len++;
  			break;
  		case 1:
  			*ancestor_out = conflict_entry;
  			len++;
  			break;
  		default:
  			break;
  		};
  	}
  
  	return len;
  }
  
  int git_index_conflict_get(
  	const git_index_entry **ancestor_out,
  	const git_index_entry **our_out,
  	const git_index_entry **their_out,
  	git_index *index,
  	const char *path)
  {
  	size_t pos;
  	int len = 0;
  
  	assert(ancestor_out && our_out && their_out && index && path);
  
  	*ancestor_out = NULL;
  	*our_out = NULL;
  	*their_out = NULL;
  
  	if (git_index_find(&pos, index, path) < 0)
  		return GIT_ENOTFOUND;
  
  	if ((len = index_conflict__get_byindex(
  		ancestor_out, our_out, their_out, index, pos)) < 0)
  		return len;
  	else if (len == 0)
  		return GIT_ENOTFOUND;
  
  	return 0;
  }
  
  int git_index_conflict_remove(git_index *index, const char *path)
  {
  	size_t pos, posmax;
  	git_index_entry *conflict_entry;
  	int error = 0;
  
  	assert(index && path);
  
  	if (git_index_find(&pos, index, path) < 0)
  		return GIT_ENOTFOUND;
  
  	posmax = git_index_entrycount(index);
  
  	while (pos < posmax) {
  		conflict_entry = git_vector_get(&index->entries, pos);
  
  		if (index->entries_cmp_path(conflict_entry->path, path) != 0)
  			break;
  
  		if (GIT_IDXENTRY_STAGE(conflict_entry) == 0) {
  			pos++;
  			continue;
  		}
  
  		if ((error = git_vector_remove(&index->entries, pos)) < 0)
  			return error;
  
  		index_entry_free(conflict_entry);
  		posmax--;
  	}
  
  	return 0;
  }
  
  static int index_conflicts_match(const git_vector *v, size_t idx)
  {
  	git_index_entry *entry = git_vector_get(v, idx);
  
  	if (GIT_IDXENTRY_STAGE(entry) > 0) {
  		index_entry_free(entry);
  		return 1;
  	}
  
  	return 0;
  }
  
  void git_index_conflict_cleanup(git_index *index)
  {
  	assert(index);
  	git_vector_remove_matching(&index->entries, index_conflicts_match);
  }
  
  int git_index_has_conflicts(const git_index *index)
  {
  	size_t i;
  	git_index_entry *entry;
  
  	assert(index);
  
  	git_vector_foreach(&index->entries, i, entry) {
  		if (GIT_IDXENTRY_STAGE(entry) > 0)
  			return 1;
  	}
  
  	return 0;
  }
  
  int git_index_conflict_iterator_new(
  	git_index_conflict_iterator **iterator_out,
  	git_index *index)
  {
  	git_index_conflict_iterator *it = NULL;
  
  	assert(iterator_out && index);
  
  	it = git__calloc(1, sizeof(git_index_conflict_iterator));
  	GITERR_CHECK_ALLOC(it);
  
  	it->index = index;
  
  	*iterator_out = it;
  	return 0;
  }
  
  int git_index_conflict_next(
  	const git_index_entry **ancestor_out,
  	const git_index_entry **our_out,
  	const git_index_entry **their_out,
  	git_index_conflict_iterator *iterator)
  {
  	const git_index_entry *entry;
  	int len;
  
  	assert(ancestor_out && our_out && their_out && iterator);
  
  	*ancestor_out = NULL;
  	*our_out = NULL;
  	*their_out = NULL;
  
  	while (iterator->cur < iterator->index->entries.length) {
  		entry = git_index_get_byindex(iterator->index, iterator->cur);
  
  		if (git_index_entry_stage(entry) > 0) {
  			if ((len = index_conflict__get_byindex(
  				ancestor_out,
  				our_out,
  				their_out,
  				iterator->index,
  				iterator->cur)) < 0)
  				return len;
  
  			iterator->cur += len;
  			return 0;
  		}
  
  		iterator->cur++;
  	}
  
  	return GIT_ITEROVER;
  }
  
  void git_index_conflict_iterator_free(git_index_conflict_iterator *iterator)
  {
  	if (iterator == NULL)
  		return;
  
  	git__free(iterator);
  }
  
  unsigned int git_index_name_entrycount(git_index *index)
  {
  	assert(index);
  	return (unsigned int)index->names.length;
  }
  
  const git_index_name_entry *git_index_name_get_byindex(
  	git_index *index, size_t n)
  {
  	assert(index);
  
  	git_vector_sort(&index->names);
  	return git_vector_get(&index->names, n);
  }
  
  int git_index_name_add(git_index *index,
  	const char *ancestor, const char *ours, const char *theirs)
  {
  	git_index_name_entry *conflict_name;
  
  	assert ((ancestor && ours) || (ancestor && theirs) || (ours && theirs));
  
  	conflict_name = git__calloc(1, sizeof(git_index_name_entry));
  	GITERR_CHECK_ALLOC(conflict_name);
  
  	if (ancestor) {
  		conflict_name->ancestor = git__strdup(ancestor);
  		GITERR_CHECK_ALLOC(conflict_name->ancestor);
  	}
  
  	if (ours) {
  		conflict_name->ours = git__strdup(ours);
  		GITERR_CHECK_ALLOC(conflict_name->ours);
  	}
  
  	if (theirs) {
  		conflict_name->theirs = git__strdup(theirs);
  		GITERR_CHECK_ALLOC(conflict_name->theirs);
  	}
  
  	return git_vector_insert(&index->names, conflict_name);
  }
  
  void git_index_name_clear(git_index *index)
  {
  	size_t i;
  	git_index_name_entry *conflict_name;
  
  	assert(index);
  
  	git_vector_foreach(&index->names, i, conflict_name) {
  		if (conflict_name->ancestor)
  			git__free(conflict_name->ancestor);
  
  		if (conflict_name->ours)
  			git__free(conflict_name->ours);
  
  		if (conflict_name->theirs)
  			git__free(conflict_name->theirs);
  
  		git__free(conflict_name);
  	}
  
  	git_vector_clear(&index->names);
  }
  
  unsigned int git_index_reuc_entrycount(git_index *index)
  {
  	assert(index);
  	return (unsigned int)index->reuc.length;
  }
  
  static int index_reuc_insert(
  	git_index *index,
  	git_index_reuc_entry *reuc,
  	int replace)
  {
  	git_index_reuc_entry **existing = NULL;
  	size_t position;
  
  	assert(index && reuc && reuc->path != NULL);
  
  	if (!git_index_reuc_find(&position, index, reuc->path))
  		existing = (git_index_reuc_entry **)&index->reuc.contents[position];
  
  	if (!replace || !existing)
  		return git_vector_insert(&index->reuc, reuc);
  
  	/* exists, replace it */
  	git__free((*existing)->path);
  	git__free(*existing);
  	*existing = reuc;
  
  	return 0;
  }
  
  int git_index_reuc_add(git_index *index, const char *path,
  	int ancestor_mode, const git_oid *ancestor_oid,
  	int our_mode, const git_oid *our_oid,
  	int their_mode, const git_oid *their_oid)
  {
  	git_index_reuc_entry *reuc = NULL;
  	int error = 0;
  
  	assert(index && path);
  
  	if ((error = index_entry_reuc_init(&reuc, path, ancestor_mode, ancestor_oid, our_mode, our_oid, their_mode, their_oid)) < 0 ||
  		(error = index_reuc_insert(index, reuc, 1)) < 0)
  	{
  		index_entry_reuc_free(reuc);
  		return error;
  	}
  
  	return error;
  } 
  
  int git_index_reuc_find(size_t *at_pos, git_index *index, const char *path)
  {
  	return git_vector_bsearch2(at_pos, &index->reuc, index->reuc_search, path);
  }
  
  const git_index_reuc_entry *git_index_reuc_get_bypath(
  	git_index *index, const char *path)
  {
  	size_t pos;
  	assert(index && path);
  
  	if (!index->reuc.length)
  		return NULL;
  
  	git_vector_sort(&index->reuc);
  
  	if (git_index_reuc_find(&pos, index, path) < 0)
  		return NULL;
  
  	return git_vector_get(&index->reuc, pos);
  }
  
  const git_index_reuc_entry *git_index_reuc_get_byindex(
  	git_index *index, size_t n)
  {
  	assert(index);
  
  	git_vector_sort(&index->reuc);
  	return git_vector_get(&index->reuc, n);
  }
  
  int git_index_reuc_remove(git_index *index, size_t position)
  {
  	int error;
  	git_index_reuc_entry *reuc;
  
  	git_vector_sort(&index->reuc);
  
  	reuc = git_vector_get(&index->reuc, position);
  	error = git_vector_remove(&index->reuc, position);
  
  	if (!error)
  		index_entry_reuc_free(reuc);
  
  	return error;
  }
  
  void git_index_reuc_clear(git_index *index)
  {
  	size_t i;
  
  	assert(index);
  
  	for (i = 0; i < index->reuc.length; ++i)
  		index_entry_reuc_free(git__swap(index->reuc.contents[i], NULL));
  
  	git_vector_clear(&index->reuc);
  }
  
  static int index_error_invalid(const char *message)
  {
  	giterr_set(GITERR_INDEX, "Invalid data in index - %s", message);
  	return -1;
  }
  
  static int read_reuc(git_index *index, const char *buffer, size_t size)
  {
  	const char *endptr;
  	size_t len;
  	int i;
  
  	/* If called multiple times, the vector might already be initialized */
  	if (index->reuc._alloc_size == 0 &&
  		git_vector_init(&index->reuc, 16, reuc_cmp) < 0)
  		return -1;
  
  	while (size) {
  		git_index_reuc_entry *lost;
  
  		len = strlen(buffer) + 1;
  		if (size <= len)
  			return index_error_invalid("reading reuc entries");
  
  		lost = git__calloc(1, sizeof(git_index_reuc_entry));
  		GITERR_CHECK_ALLOC(lost);
  
  		/* read NUL-terminated pathname for entry */
  		lost->path = git__strdup(buffer);
  		GITERR_CHECK_ALLOC(lost->path);
  
  		size -= len;
  		buffer += len;
  
  		/* read 3 ASCII octal numbers for stage entries */
  		for (i = 0; i < 3; i++) {
  			int tmp;
  
  			if (git__strtol32(&tmp, buffer, &endptr, 8) < 0 ||
  				!endptr || endptr == buffer || *endptr ||
  				(unsigned)tmp > UINT_MAX) {
  				index_entry_reuc_free(lost);
  				return index_error_invalid("reading reuc entry stage");
  			}
  
  			lost->mode[i] = tmp;
  
  			len = (endptr + 1) - buffer;
  			if (size <= len) {
  				index_entry_reuc_free(lost);
  				return index_error_invalid("reading reuc entry stage");
  			}
  
  			size -= len;
  			buffer += len;
  		}
  
  		/* read up to 3 OIDs for stage entries */
  		for (i = 0; i < 3; i++) {
  			if (!lost->mode[i])
  				continue;
  			if (size < 20) {
  				index_entry_reuc_free(lost);
  				return index_error_invalid("reading reuc entry oid");
  			}
  
  			git_oid_fromraw(&lost->oid[i], (const unsigned char *) buffer);
  			size -= 20;
  			buffer += 20;
  		}
  
  		/* entry was read successfully - insert into reuc vector */
  		if (git_vector_insert(&index->reuc, lost) < 0)
  			return -1;
  	}
  
  	/* entries are guaranteed to be sorted on-disk */
  	index->reuc.sorted = 1;
  
  	return 0;
  }
  
  
  static int read_conflict_names(git_index *index, const char *buffer, size_t size)
  {
  	size_t len;
  
  	/* This gets called multiple times, the vector might already be initialized */
  	if (index->names._alloc_size == 0 &&
  		git_vector_init(&index->names, 16, conflict_name_cmp) < 0)
  		return -1;
  
  #define read_conflict_name(ptr) \
  	len = strlen(buffer) + 1; \
  	if (size < len) \
  		return index_error_invalid("reading conflict name entries"); \
  	\
  	if (len == 1) \
  		ptr = NULL; \
  	else { \
  		ptr = git__malloc(len); \
  		GITERR_CHECK_ALLOC(ptr); \
  		memcpy(ptr, buffer, len); \
  	} \
  	\
  	buffer += len; \
  	size -= len;
  
  	while (size) {
  		git_index_name_entry *conflict_name = git__calloc(1, sizeof(git_index_name_entry));
  		GITERR_CHECK_ALLOC(conflict_name);
  
  		read_conflict_name(conflict_name->ancestor);
  		read_conflict_name(conflict_name->ours);
  		read_conflict_name(conflict_name->theirs);
  
  		if (git_vector_insert(&index->names, conflict_name) < 0)
  			return -1;
  	}
  
  #undef read_conflict_name
  
  	/* entries are guaranteed to be sorted on-disk */
  	index->names.sorted = 1;
  
  	return 0;
  }
  
  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 index_error_invalid("incorrect header signature");
  
  	dest->version = ntohl(source->version);
  	if (dest->version != INDEX_VERSION_NUMBER_EXT &&
  		dest->version != INDEX_VERSION_NUMBER)
  		return index_error_invalid("incorrect header version");
  
  	dest->entry_count = ntohl(source->entry_count);
  	return 0;
  }
  
  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 ||
  		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 (git_tree_cache_read(&index->tree, buffer + 8, dest.extension_size) < 0)
  				return 0;
  		} else if (memcmp(dest.signature, INDEX_EXT_UNMERGED_SIG, 4) == 0) {
  			if (read_reuc(index, buffer + 8, dest.extension_size) < 0)
  				return 0;
  		} else if (memcmp(dest.signature, INDEX_EXT_CONFLICT_NAME_SIG, 4) == 0) {
  			if (read_conflict_names(index, buffer + 8, dest.extension_size) < 0)
  				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 = { 0 };
  	git_oid checksum_calculated, checksum_expected;
  
  #define seek_forward(_increase) { \
  	if (_increase >= buffer_size) \
  		return index_error_invalid("ran out of data while parsing"); \
  	buffer += _increase; \
  	buffer_size -= _increase;\
  }
  
  	if (buffer_size < INDEX_HEADER_SIZE + INDEX_FOOTER_SIZE)
  		return index_error_invalid("insufficient buffer space");
  
  	/* 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) < 0)
  		return -1;
  
  	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));
  		GITERR_CHECK_ALLOC(entry);
  
  		entry_size = read_entry(entry, buffer, buffer_size);
  
  		/* 0 bytes read means an object corruption */
  		if (entry_size == 0)
  			return index_error_invalid("invalid entry");
  
  		if (git_vector_insert(&index->entries, entry) < 0)
  			return -1;
  
  		seek_forward(entry_size);
  	}
  
  	if (i != header.entry_count)
  		return index_error_invalid("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 index_error_invalid("extension is truncated");
  
  		seek_forward(extension_size);
  	}
  
  	if (buffer_size != INDEX_FOOTER_SIZE)
  		return index_error_invalid("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 index_error_invalid("calculated checksum does not match expected");
  
  #undef seek_forward
  
  	/* Entries are stored case-sensitively on disk. */
  	index->entries.sorted = !index->ignore_case;
  	git_vector_sort(&index->entries);
  
  	return 0;
  }
  
  static bool is_index_extended(git_index *index)
  {
  	size_t i, extended;
  	git_index_entry *entry;
  
  	extended = 0;
  
  	git_vector_foreach(&index->entries, i, entry) {
  		entry->flags &= ~GIT_IDXENTRY_EXTENDED;
  		if (entry->flags_extended & GIT_IDXENTRY_EXTENDED_FLAGS) {
  			extended++;
  			entry->flags |= GIT_IDXENTRY_EXTENDED;
  		}
  	}
  
  	return (extended > 0);
  }
  
  static int write_disk_entry(git_filebuf *file, git_index_entry *entry)
  {
  	void *mem = NULL;
  	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, &mem, disk_size) < 0)
  		return -1;
  
  	ondisk = (struct entry_short *)mem;
  
  	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 0;
  }
  
  static int write_entries(git_index *index, git_filebuf *file)
  {
  	int error = 0;
  	size_t i;
  	git_vector case_sorted;
  	git_index_entry *entry;
  	git_vector *out = &index->entries;
  
  	/* If index->entries is sorted case-insensitively, then we need
  	 * to re-sort it case-sensitively before writing */
  	if (index->ignore_case) {
  		git_vector_dup(&case_sorted, &index->entries, index_cmp);
  		git_vector_sort(&case_sorted);
  		out = &case_sorted;
  	}
  
  	git_vector_foreach(out, i, entry)
  		if ((error = write_disk_entry(file, entry)) < 0)
  			break;
  
  	if (index->ignore_case)
  		git_vector_free(&case_sorted);
  
  	return error;
  }
  
  static int write_extension(git_filebuf *file, struct index_extension *header, git_buf *data)
  {
  	struct index_extension ondisk;
  	int error = 0;
  
  	memset(&ondisk, 0x0, sizeof(struct index_extension));
  	memcpy(&ondisk, header, 4);
  	ondisk.extension_size = htonl(header->extension_size);
  
  	if ((error = git_filebuf_write(file, &ondisk, sizeof(struct index_extension))) == 0)
  		error = git_filebuf_write(file, data->ptr, data->size);
  
  	return error;
  }
  
  static int create_name_extension_data(git_buf *name_buf, git_index_name_entry *conflict_name)
  {
  	int error = 0;
  
  	if (conflict_name->ancestor == NULL)
  		error = git_buf_put(name_buf, "\0", 1);
  	else
  		error = git_buf_put(name_buf, conflict_name->ancestor, strlen(conflict_name->ancestor) + 1);
  
  	if (error != 0)
  		goto on_error;
  
  	if (conflict_name->ours == NULL)
  		error = git_buf_put(name_buf, "\0", 1);
  	else
  		error = git_buf_put(name_buf, conflict_name->ours, strlen(conflict_name->ours) + 1);
  
  	if (error != 0)
  		goto on_error;
  
  	if (conflict_name->theirs == NULL)
  		error = git_buf_put(name_buf, "\0", 1);
  	else
  		error = git_buf_put(name_buf, conflict_name->theirs, strlen(conflict_name->theirs) + 1);
  
  on_error:
  	return error;
  }
  
  static int write_name_extension(git_index *index, git_filebuf *file)
  {
  	git_buf name_buf = GIT_BUF_INIT;
  	git_vector *out = &index->names;
  	git_index_name_entry *conflict_name;
  	struct index_extension extension;
  	size_t i;
  	int error = 0;
  
  	git_vector_foreach(out, i, conflict_name) {
  		if ((error = create_name_extension_data(&name_buf, conflict_name)) < 0)
  			goto done;
  	}
  
  	memset(&extension, 0x0, sizeof(struct index_extension));
  	memcpy(&extension.signature, INDEX_EXT_CONFLICT_NAME_SIG, 4);
  	extension.extension_size = (uint32_t)name_buf.size;
  
  	error = write_extension(file, &extension, &name_buf);
  
  	git_buf_free(&name_buf);
  
  done:
  	return error;
  }
  
  static int create_reuc_extension_data(git_buf *reuc_buf, git_index_reuc_entry *reuc)
  {
  	int i;
  	int error = 0;
  
  	if ((error = git_buf_put(reuc_buf, reuc->path, strlen(reuc->path) + 1)) < 0)
  		return error;
  
  	for (i = 0; i < 3; i++) {
  		if ((error = git_buf_printf(reuc_buf, "%o", reuc->mode[i])) < 0 ||
  			(error = git_buf_put(reuc_buf, "\0", 1)) < 0)
  			return error;
  	}
  
  	for (i = 0; i < 3; i++) {
  		if (reuc->mode[i] && (error = git_buf_put(reuc_buf, (char *)&reuc->oid[i].id, GIT_OID_RAWSZ)) < 0)
  			return error;
  	}
  
  	return 0;
  }
  
  static int write_reuc_extension(git_index *index, git_filebuf *file)
  {
  	git_buf reuc_buf = GIT_BUF_INIT;
  	git_vector *out = &index->reuc;
  	git_index_reuc_entry *reuc;
  	struct index_extension extension;
  	size_t i;
  	int error = 0;
  
  	git_vector_foreach(out, i, reuc) {
  		if ((error = create_reuc_extension_data(&reuc_buf, reuc)) < 0)
  			goto done;
  	}
  
  	memset(&extension, 0x0, sizeof(struct index_extension));
  	memcpy(&extension.signature, INDEX_EXT_UNMERGED_SIG, 4);
  	extension.extension_size = (uint32_t)reuc_buf.size;
  
  	error = write_extension(file, &extension, &reuc_buf);
  
  	git_buf_free(&reuc_buf);
  
  done:
  	return error;
  }
  
  static int write_index(git_index *index, git_filebuf *file)
  {
  	git_oid hash_final;
  	struct index_header header;
  	bool 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((uint32_t)index->entries.length);
  
  	if (git_filebuf_write(file, &header, sizeof(struct index_header)) < 0)
  		return -1;
  
  	if (write_entries(index, file) < 0)
  		return -1;
  
  	/* TODO: write tree cache extension */
  
  	/* write the rename conflict extension */
  	if (index->names.length > 0 && write_name_extension(index, file) < 0)
  		return -1;
  
  	/* write the reuc extension */
  	if (index->reuc.length > 0 && write_reuc_extension(index, file) < 0)
  		return -1;
  
  	/* 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 */
  	return git_filebuf_write(file, hash_final.id, GIT_OID_RAWSZ);
  }
  
  int git_index_entry_stage(const git_index_entry *entry)
  {
  	return GIT_IDXENTRY_STAGE(entry);
  }
  
  typedef struct read_tree_data {
  	git_vector *old_entries;
  	git_vector *new_entries;
  	git_vector_cmp entries_search;
  } read_tree_data;
  
  static int read_tree_cb(
  	const char *root, const git_tree_entry *tentry, void *payload)
  {
  	read_tree_data *data = payload;
  	git_index_entry *entry = NULL, *old_entry;
  	git_buf path = GIT_BUF_INIT;
  
  	if (git_tree_entry__is_tree(tentry))
  		return 0;
  
  	if (git_buf_joinpath(&path, root, tentry->filename) < 0)
  		return -1;
  
  	entry = git__calloc(1, sizeof(git_index_entry));
  	GITERR_CHECK_ALLOC(entry);
  
  	entry->mode = tentry->attr;
  	entry->oid = tentry->oid;
  
  	/* look for corresponding old entry and copy data to new entry */
  	if (data->old_entries) {
  		size_t pos;
  		struct entry_srch_key skey;
  
  		skey.path = path.ptr;
  		skey.stage = 0;
  
  		if (!git_vector_bsearch2(
  				&pos, data->old_entries, data->entries_search, &skey) &&
  			(old_entry = git_vector_get(data->old_entries, pos)) != NULL &&
  			entry->mode == old_entry->mode &&
  			git_oid_equal(&entry->oid, &old_entry->oid))
  		{
  			memcpy(entry, old_entry, sizeof(*entry));
  			entry->flags_extended = 0;
  		}
  	}
  
  	if (path.size < GIT_IDXENTRY_NAMEMASK)
  		entry->flags = path.size & GIT_IDXENTRY_NAMEMASK;
  	else
  		entry->flags = GIT_IDXENTRY_NAMEMASK;
  
  	entry->path = git_buf_detach(&path);
  	git_buf_free(&path);
  
  	if (git_vector_insert(data->new_entries, entry) < 0) {
  		index_entry_free(entry);
  		return -1;
  	}
  
  	return 0;
  }
  
  int git_index_read_tree(git_index *index, const git_tree *tree)
  {
  	int error = 0;
  	git_vector entries = GIT_VECTOR_INIT;
  	read_tree_data data;
  
  	git_vector_set_cmp(&entries, index->entries._cmp); /* match sort */
  
  	data.old_entries = &index->entries;
  	data.new_entries = &entries;
  	data.entries_search = index->entries_search;
  
  	git_vector_sort(&index->entries);
  
  	error = git_tree_walk(tree, GIT_TREEWALK_POST, read_tree_cb, &data);
  
  	git_vector_sort(&entries);
  
  	git_index_clear(index);
  
  	git_vector_swap(&entries, &index->entries);
  	git_vector_free(&entries);
  
  	return error;
  }
  
  git_repository *git_index_owner(const git_index *index)
  {
  	return INDEX_OWNER(index);
  }
  
  int git_index_add_all(
  	git_index *index,
  	const git_strarray *paths,
  	unsigned int flags,
  	git_index_matched_path_cb cb,
  	void *payload)
  {
  	int error;
  	git_repository *repo;
  	git_iterator *wditer = NULL;
  	const git_index_entry *wd = NULL;
  	git_index_entry *entry;
  	git_pathspec ps;
  	const char *match;
  	size_t existing;
  	bool no_fnmatch = (flags & GIT_INDEX_ADD_DISABLE_PATHSPEC_MATCH) != 0;
  	int ignorecase;
  	git_oid blobid;
  
  	assert(index);
  
  	if (INDEX_OWNER(index) == NULL)
  		return create_index_error(-1,
  			"Could not add paths to index. "
  			"Index is not backed up by an existing repository.");
  
  	repo = INDEX_OWNER(index);
  	if ((error = git_repository__ensure_not_bare(repo, "index add all")) < 0)
  		return error;
  
  	if (git_repository__cvar(&ignorecase, repo, GIT_CVAR_IGNORECASE) < 0)
  		return -1;
  
  	if ((error = git_pathspec__init(&ps, paths)) < 0)
  		return error;
  
  	/* optionally check that pathspec doesn't mention any ignored files */
  	if ((flags & GIT_INDEX_ADD_CHECK_PATHSPEC) != 0 &&
  		(flags & GIT_INDEX_ADD_FORCE) == 0 &&
  		(error = git_ignore__check_pathspec_for_exact_ignores(
  			repo, &ps.pathspec, no_fnmatch)) < 0)
  		goto cleanup;
  
  	if ((error = git_iterator_for_workdir(
  			&wditer, repo, 0, ps.prefix, ps.prefix)) < 0)
  		goto cleanup;
  
  	while (!(error = git_iterator_advance(&wd, wditer))) {
  
  		/* check if path actually matches */
  		if (!git_pathspec__match(
  				&ps.pathspec, wd->path, no_fnmatch, ignorecase, &match, NULL))
  			continue;
  
  		/* skip ignored items that are not already in the index */
  		if ((flags & GIT_INDEX_ADD_FORCE) == 0 &&
  			git_iterator_current_is_ignored(wditer) &&
  			git_index__find(&existing, index, wd->path, 0) < 0)
  			continue;
  
  		/* issue notification callback if requested */
  		if (cb && (error = cb(wd->path, match, payload)) != 0) {
  			if (error > 0) /* return > 0 means skip this one */
  				continue;
  			if (error < 0) { /* return < 0 means abort */
  				giterr_clear();
  				error = GIT_EUSER;
  				break;
  			}
  		}
  
  		/* TODO: Should we check if the file on disk is already an exact
  		 * match to the file in the index and skip this work if it is?
  		 */
  
  		/* write the blob to disk and get the oid */
  		if ((error = git_blob_create_fromworkdir(&blobid, repo, wd->path)) < 0)
  			break;
  
  		/* make the new entry to insert */
  		if ((entry = index_entry_dup(wd)) == NULL) {
  			error = -1;
  			break;
  		}
  		entry->oid = blobid;
  
  		/* add working directory item to index */
  		if ((error = index_insert(index, entry, 1)) < 0) {
  			index_entry_free(entry);
  			break;
  		}
  
  		git_tree_cache_invalidate_path(index->tree, wd->path);
  
  		/* add implies conflict resolved, move conflict entries to REUC */
  		if ((error = index_conflict_to_reuc(index, wd->path)) < 0) {
  			if (error != GIT_ENOTFOUND)
  				break;
  			giterr_clear();
  		}
  	}
  
  	if (error == GIT_ITEROVER)
  		error = 0;
  
  cleanup:
  	git_iterator_free(wditer);
  	git_pathspec__clear(&ps);
  
  	return error;
  }
  
  enum {
  	INDEX_ACTION_NONE = 0,
  	INDEX_ACTION_UPDATE = 1,
  	INDEX_ACTION_REMOVE = 2,
  };
  
  static int index_apply_to_all(
  	git_index *index,
  	int action,
  	const git_strarray *paths,
  	git_index_matched_path_cb cb,
  	void *payload)
  {
  	int error = 0;
  	size_t i;
  	git_pathspec ps;
  	const char *match;
  	git_buf path = GIT_BUF_INIT;
  
  	assert(index);
  
  	if ((error = git_pathspec__init(&ps, paths)) < 0)
  		return error;
  
  	git_vector_sort(&index->entries);
  
  	for (i = 0; !error && i < index->entries.length; ++i) {
  		git_index_entry *entry = git_vector_get(&index->entries, i);
  
  		/* check if path actually matches */
  		if (!git_pathspec__match(
  				&ps.pathspec, entry->path, false, index->ignore_case,
  				&match, NULL))
  			continue;
  
  		/* issue notification callback if requested */
  		if (cb && (error = cb(entry->path, match, payload)) != 0) {
  			if (error > 0) { /* return > 0 means skip this one */
  				error = 0;
  				continue;
  			}
  			if (error < 0) { /* return < 0 means abort */
  				giterr_clear();
  				error = GIT_EUSER;
  				break;
  			}
  		}
  
  		/* index manipulation may alter entry, so don't depend on it */
  		if ((error = git_buf_sets(&path, entry->path)) < 0)
  			break;
  
  		switch (action) {
  		case INDEX_ACTION_NONE:
  			break;
  		case INDEX_ACTION_UPDATE:
  			error = git_index_add_bypath(index, path.ptr);
  
  			if (error == GIT_ENOTFOUND) {
  				giterr_clear();
  
  				error = git_index_remove_bypath(index, path.ptr);
  
  				if (!error) /* back up foreach if we removed this */
  					i--;
  			}
  			break;
  		case INDEX_ACTION_REMOVE:
  			if (!(error = git_index_remove_bypath(index, path.ptr)))
  				i--; /* back up foreach if we removed this */
  			break;
  		default:
  			giterr_set(GITERR_INVALID, "Unknown index action %d", action);
  			error = -1;
  			break;
  		}
  	}
  
  	git_buf_free(&path);
  	git_pathspec__clear(&ps);
  
  	return error;
  }
  
  int git_index_remove_all(
  	git_index *index,
  	const git_strarray *pathspec,
  	git_index_matched_path_cb cb,
  	void *payload)
  {
  	return index_apply_to_all(
  		index, INDEX_ACTION_REMOVE, pathspec, cb, payload);
  }
  
  int git_index_update_all(
  	git_index *index,
  	const git_strarray *pathspec,
  	git_index_matched_path_cb cb,
  	void *payload)
  {
  	return index_apply_to_all(
  		index, INDEX_ACTION_UPDATE, pathspec, cb, payload);
  }
  