/*
 * GIT - The information manager from hell
 *
 * Copyright (C) Linus Torvalds, 2005
 */
#define NO_THE_INDEX_COMPATIBILITY_MACROS
#include "cache.h"
#include "cache-tree.h"
#include "refs.h"
#include "dir.h"

/* Index extensions.
 *
 * The first letter should be 'A'..'Z' for extensions that are not
 * necessary for a correct operation (i.e. optimization data).
 * When new extensions are added that _needs_ to be understood in
 * order to correctly interpret the index file, pick character that
 * is outside the range, to cause the reader to abort.
 */

#define CACHE_EXT(s) ( (s[0]<<24)|(s[1]<<16)|(s[2]<<8)|(s[3]) )
#define CACHE_EXT_TREE 0x54524545       /* "TREE" */

struct index_state the_index;

static void set_index_entry(struct index_state *istate, int nr, struct cache_entry *ce)
{
        istate->cache[nr] = ce;
        add_name_hash(istate, ce);
}

static void replace_index_entry(struct index_state *istate, int nr, struct cache_entry *ce)
{
        struct cache_entry *old = istate->cache[nr];

        remove_name_hash(old);
        set_index_entry(istate, nr, ce);
        istate->cache_changed = 1;
}

/*
 * This only updates the "non-critical" parts of the directory
 * cache, ie the parts that aren't tracked by GIT, and only used
 * to validate the cache.
 */
void fill_stat_cache_info(struct cache_entry *ce, struct stat *st)
{
        ce->ce_ctime = st->st_ctime;
        ce->ce_mtime = st->st_mtime;
        ce->ce_dev = st->st_dev;
        ce->ce_ino = st->st_ino;
        ce->ce_uid = st->st_uid;
        ce->ce_gid = st->st_gid;
        ce->ce_size = st->st_size;

        if (assume_unchanged)
                ce->ce_flags |= CE_VALID;

        if (S_ISREG(st->st_mode))
                ce_mark_uptodate(ce);
}

static int ce_compare_data(struct cache_entry *ce, struct stat *st)
{
        int match = -1;
        int fd = open(ce->name, O_RDONLY);

        if (fd >= 0) {
                unsigned char sha1[20];
                if (!index_fd(sha1, fd, st, 0, OBJ_BLOB, ce->name))
                        match = hashcmp(sha1, ce->sha1);
                /* index_fd() closed the file descriptor already */
        }
        return match;
}

static int ce_compare_link(struct cache_entry *ce, size_t expected_size)
{
        int match = -1;
        char *target;
        void *buffer;
        unsigned long size;
        enum object_type type;
        int len;

        target = xmalloc(expected_size);
        len = readlink(ce->name, target, expected_size);
        if (len != expected_size) {
                free(target);
                return -1;
        }
        buffer = read_sha1_file(ce->sha1, &type, &size);
        if (!buffer) {
                free(target);
                return -1;
        }
        if (size == expected_size)
                match = memcmp(buffer, target, size);
        free(buffer);
        free(target);
        return match;
}

static int ce_compare_gitlink(struct cache_entry *ce)
{
        unsigned char sha1[20];

        /*
         * We don't actually require that the .git directory
         * under GITLINK directory be a valid git directory. It
         * might even be missing (in case nobody populated that
         * sub-project).
         *
         * If so, we consider it always to match.
         */
        if (resolve_gitlink_ref(ce->name, "HEAD", sha1) < 0)
                return 0;
        return hashcmp(sha1, ce->sha1);
}

static int ce_modified_check_fs(struct cache_entry *ce, struct stat *st)
{
        switch (st->st_mode & S_IFMT) {
        case S_IFREG:
                if (ce_compare_data(ce, st))
                        return DATA_CHANGED;
                break;
        case S_IFLNK:
                if (ce_compare_link(ce, xsize_t(st->st_size)))
                        return DATA_CHANGED;
                break;
        case S_IFDIR:
                if (S_ISGITLINK(ce->ce_mode))
                        return 0;
        default:
                return TYPE_CHANGED;
        }
        return 0;
}

static int ce_match_stat_basic(struct cache_entry *ce, struct stat *st)
{
        unsigned int changed = 0;

        if (ce->ce_flags & CE_REMOVE)
                return MODE_CHANGED | DATA_CHANGED | TYPE_CHANGED;

        switch (ce->ce_mode & S_IFMT) {
        case S_IFREG:
                changed |= !S_ISREG(st->st_mode) ? TYPE_CHANGED : 0;
                /* We consider only the owner x bit to be relevant for
                 * "mode changes"
                 */
                if (trust_executable_bit &&
                    (0100 & (ce->ce_mode ^ st->st_mode)))
                        changed |= MODE_CHANGED;
                break;
        case S_IFLNK:
                if (!S_ISLNK(st->st_mode) &&
                    (has_symlinks || !S_ISREG(st->st_mode)))
                        changed |= TYPE_CHANGED;
                break;
        case S_IFGITLINK:
                if (!S_ISDIR(st->st_mode))
                        changed |= TYPE_CHANGED;
                else if (ce_compare_gitlink(ce))
                        changed |= DATA_CHANGED;
                return changed;
        default:
                die("internal error: ce_mode is %o", ce->ce_mode);
        }
        if (ce->ce_mtime != (unsigned int) st->st_mtime)
                changed |= MTIME_CHANGED;
        if (ce->ce_ctime != (unsigned int) st->st_ctime)
                changed |= CTIME_CHANGED;

        if (ce->ce_uid != (unsigned int) st->st_uid ||
            ce->ce_gid != (unsigned int) st->st_gid)
                changed |= OWNER_CHANGED;
        if (ce->ce_ino != (unsigned int) st->st_ino)
                changed |= INODE_CHANGED;

#ifdef USE_STDEV
        /*
         * st_dev breaks on network filesystems where different
         * clients will have different views of what "device"
         * the filesystem is on
         */
        if (ce->ce_dev != (unsigned int) st->st_dev)
                changed |= INODE_CHANGED;
#endif

        if (ce->ce_size != (unsigned int) st->st_size)
                changed |= DATA_CHANGED;

        return changed;
}

static int is_racy_timestamp(const struct index_state *istate, struct cache_entry *ce)
{
        return (istate->timestamp &&
                ((unsigned int)istate->timestamp) <= ce->ce_mtime);
}

int ie_match_stat(const struct index_state *istate,
                  struct cache_entry *ce, struct stat *st,
                  unsigned int options)
{
        unsigned int changed;
        int ignore_valid = options & CE_MATCH_IGNORE_VALID;
        int assume_racy_is_modified = options & CE_MATCH_RACY_IS_DIRTY;

        /*
         * If it's marked as always valid in the index, it's
         * valid whatever the checked-out copy says.
         */
        if (!ignore_valid && (ce->ce_flags & CE_VALID))
                return 0;

        changed = ce_match_stat_basic(ce, st);

        /*
         * Within 1 second of this sequence:
         *      echo xyzzy >file && git-update-index --add file
         * running this command:
         *      echo frotz >file
         * would give a falsely clean cache entry.  The mtime and
         * length match the cache, and other stat fields do not change.
         *
         * We could detect this at update-index time (the cache entry
         * being registered/updated records the same time as "now")
         * and delay the return from git-update-index, but that would
         * effectively mean we can make at most one commit per second,
         * which is not acceptable.  Instead, we check cache entries
         * whose mtime are the same as the index file timestamp more
         * carefully than others.
         */
        if (!changed && is_racy_timestamp(istate, ce)) {
                if (assume_racy_is_modified)
                        changed |= DATA_CHANGED;
                else
                        changed |= ce_modified_check_fs(ce, st);
        }

        return changed;
}

int ie_modified(const struct index_state *istate,
                struct cache_entry *ce, struct stat *st, unsigned int options)
{
        int changed, changed_fs;

        changed = ie_match_stat(istate, ce, st, options);
        if (!changed)
                return 0;
        /*
         * If the mode or type has changed, there's no point in trying
         * to refresh the entry - it's not going to match
         */
        if (changed & (MODE_CHANGED | TYPE_CHANGED))
                return changed;

        /* Immediately after read-tree or update-index --cacheinfo,
         * the length field is zero.  For other cases the ce_size
         * should match the SHA1 recorded in the index entry.
         */
        if ((changed & DATA_CHANGED) && ce->ce_size != 0)
                return changed;

        changed_fs = ce_modified_check_fs(ce, st);
        if (changed_fs)
                return changed | changed_fs;
        return 0;
}

int base_name_compare(const char *name1, int len1, int mode1,
                      const char *name2, int len2, int mode2)
{
        unsigned char c1, c2;
        int len = len1 < len2 ? len1 : len2;
        int cmp;

        cmp = memcmp(name1, name2, len);
        if (cmp)
                return cmp;
        c1 = name1[len];
        c2 = name2[len];
        if (!c1 && S_ISDIR(mode1))
                c1 = '/';
        if (!c2 && S_ISDIR(mode2))
                c2 = '/';
        return (c1 < c2) ? -1 : (c1 > c2) ? 1 : 0;
}

/*
 * df_name_compare() is identical to base_name_compare(), except it
 * compares conflicting directory/file entries as equal. Note that
 * while a directory name compares as equal to a regular file, they
 * then individually compare _differently_ to a filename that has
 * a dot after the basename (because '\0' < '.' < '/').
 *
 * This is used by routines that want to traverse the git namespace
 * but then handle conflicting entries together when possible.
 */
int df_name_compare(const char *name1, int len1, int mode1,
                    const char *name2, int len2, int mode2)
{
        int len = len1 < len2 ? len1 : len2, cmp;
        unsigned char c1, c2;

        cmp = memcmp(name1, name2, len);
        if (cmp)
                return cmp;
        /* Directories and files compare equal (same length, same name) */
        if (len1 == len2)
                return 0;
        c1 = name1[len];
        if (!c1 && S_ISDIR(mode1))
                c1 = '/';
        c2 = name2[len];
        if (!c2 && S_ISDIR(mode2))
                c2 = '/';
        if (c1 == '/' && !c2)
                return 0;
        if (c2 == '/' && !c1)
                return 0;
        return c1 - c2;
}

int cache_name_compare(const char *name1, int flags1, const char *name2, int flags2)
{
        int len1 = flags1 & CE_NAMEMASK;
        int len2 = flags2 & CE_NAMEMASK;
        int len = len1 < len2 ? len1 : len2;
        int cmp;

        cmp = memcmp(name1, name2, len);
        if (cmp)
                return cmp;
        if (len1 < len2)
                return -1;
        if (len1 > len2)
                return 1;

        /* Compare stages  */
        flags1 &= CE_STAGEMASK;
        flags2 &= CE_STAGEMASK;

        if (flags1 < flags2)
                return -1;
        if (flags1 > flags2)
                return 1;
        return 0;
}

int index_name_pos(const struct index_state *istate, const char *name, int namelen)
{
        int first, last;

        first = 0;
        last = istate->cache_nr;
        while (last > first) {
                int next = (last + first) >> 1;
                struct cache_entry *ce = istate->cache[next];
                int cmp = cache_name_compare(name, namelen, ce->name, ce->ce_flags);
                if (!cmp)
                        return next;
                if (cmp < 0) {
                        last = next;
                        continue;
                }
                first = next+1;
        }
        return -first-1;
}

/* Remove entry, return true if there are more entries to go.. */
int remove_index_entry_at(struct index_state *istate, int pos)
{
        struct cache_entry *ce = istate->cache[pos];

        remove_name_hash(ce);
        istate->cache_changed = 1;
        istate->cache_nr--;
        if (pos >= istate->cache_nr)
                return 0;
        memmove(istate->cache + pos,
                istate->cache + pos + 1,
                (istate->cache_nr - pos) * sizeof(struct cache_entry *));
        return 1;
}

int remove_file_from_index(struct index_state *istate, const char *path)
{
        int pos = index_name_pos(istate, path, strlen(path));
        if (pos < 0)
                pos = -pos-1;
        cache_tree_invalidate_path(istate->cache_tree, path);
        while (pos < istate->cache_nr && !strcmp(istate->cache[pos]->name, path))
                remove_index_entry_at(istate, pos);
        return 0;
}

static int compare_name(struct cache_entry *ce, const char *path, int namelen)
{
        return namelen != ce_namelen(ce) || memcmp(path, ce->name, namelen);
}

static int index_name_pos_also_unmerged(struct index_state *istate,
        const char *path, int namelen)
{
        int pos = index_name_pos(istate, path, namelen);
        struct cache_entry *ce;

        if (pos >= 0)
                return pos;

        /* maybe unmerged? */
        pos = -1 - pos;
        if (pos >= istate->cache_nr ||
                        compare_name((ce = istate->cache[pos]), path, namelen))
                return -1;

        /* order of preference: stage 2, 1, 3 */
        if (ce_stage(ce) == 1 && pos + 1 < istate->cache_nr &&
                        ce_stage((ce = istate->cache[pos + 1])) == 2 &&
                        !compare_name(ce, path, namelen))
                pos++;
        return pos;
}

int add_file_to_index(struct index_state *istate, const char *path, int verbose)
{
        int size, namelen;
        struct stat st;
        struct cache_entry *ce, *alias;
        unsigned ce_option = CE_MATCH_IGNORE_VALID|CE_MATCH_RACY_IS_DIRTY;

        if (lstat(path, &st))
                die("%s: unable to stat (%s)", path, strerror(errno));

        if (!S_ISREG(st.st_mode) && !S_ISLNK(st.st_mode) && !S_ISDIR(st.st_mode))
                die("%s: can only add regular files, symbolic links or git-directories", path);

        namelen = strlen(path);
        if (S_ISDIR(st.st_mode)) {
                while (namelen && path[namelen-1] == '/')
                        namelen--;
        }
        size = cache_entry_size(namelen);
        ce = xcalloc(1, size);
        memcpy(ce->name, path, namelen);
        ce->ce_flags = namelen;
        fill_stat_cache_info(ce, &st);

        if (trust_executable_bit && has_symlinks)
                ce->ce_mode = create_ce_mode(st.st_mode);
        else {
                /* If there is an existing entry, pick the mode bits and type
                 * from it, otherwise assume unexecutable regular file.
                 */
                struct cache_entry *ent;
                int pos = index_name_pos_also_unmerged(istate, path, namelen);

                ent = (0 <= pos) ? istate->cache[pos] : NULL;
                ce->ce_mode = ce_mode_from_stat(ent, st.st_mode);
        }

        alias = index_name_exists(istate, ce->name, ce_namelen(ce), ignore_case);
        if (alias && !ce_stage(alias) && !ie_match_stat(istate, alias, &st, ce_option)) {
                /* Nothing changed, really */
                free(ce);
                ce_mark_uptodate(alias);
                return 0;
        }

        if (index_path(ce->sha1, path, &st, 1))
                die("unable to index file %s", path);
        if (add_index_entry(istate, ce, ADD_CACHE_OK_TO_ADD|ADD_CACHE_OK_TO_REPLACE))
                die("unable to add %s to index",path);
        if (verbose)
                printf("add '%s'\n", path);
        return 0;
}

struct cache_entry *make_cache_entry(unsigned int mode,
                const unsigned char *sha1, const char *path, int stage,
                int refresh)
{
        int size, len;
        struct cache_entry *ce;

        if (!verify_path(path))
                return NULL;

        len = strlen(path);
        size = cache_entry_size(len);
        ce = xcalloc(1, size);

        hashcpy(ce->sha1, sha1);
        memcpy(ce->name, path, len);
        ce->ce_flags = create_ce_flags(len, stage);
        ce->ce_mode = create_ce_mode(mode);

        if (refresh)
                return refresh_cache_entry(ce, 0);

        return ce;
}

int ce_same_name(struct cache_entry *a, struct cache_entry *b)
{
        int len = ce_namelen(a);
        return ce_namelen(b) == len && !memcmp(a->name, b->name, len);
}

int ce_path_match(const struct cache_entry *ce, const char **pathspec)
{
        const char *match, *name;
        int len;

        if (!pathspec)
                return 1;

        len = ce_namelen(ce);
        name = ce->name;
        while ((match = *pathspec++) != NULL) {
                int matchlen = strlen(match);
                if (matchlen > len)
                        continue;
                if (memcmp(name, match, matchlen))
                        continue;
                if (matchlen && name[matchlen-1] == '/')
                        return 1;
                if (name[matchlen] == '/' || !name[matchlen])
                        return 1;
                if (!matchlen)
                        return 1;
        }
        return 0;
}

/*
 * We fundamentally don't like some paths: we don't want
 * dot or dot-dot anywhere, and for obvious reasons don't
 * want to recurse into ".git" either.
 *
 * Also, we don't want double slashes or slashes at the
 * end that can make pathnames ambiguous.
 */
static int verify_dotfile(const char *rest)
{
        /*
         * The first character was '.', but that
         * has already been discarded, we now test
         * the rest.
         */
        switch (*rest) {
        /* "." is not allowed */
        case '\0': case '/':
                return 0;

        /*
         * ".git" followed by  NUL or slash is bad. This
         * shares the path end test with the ".." case.
         */
        case 'g':
                if (rest[1] != 'i')
                        break;
                if (rest[2] != 't')
                        break;
                rest += 2;
        /* fallthrough */
        case '.':
                if (rest[1] == '\0' || rest[1] == '/')
                        return 0;
        }
        return 1;
}

int verify_path(const char *path)
{
        char c;

        goto inside;
        for (;;) {
                if (!c)
                        return 1;
                if (c == '/') {
inside:
                        c = *path++;
                        switch (c) {
                        default:
                                continue;
                        case '/': case '\0':
                                break;
                        case '.':
                                if (verify_dotfile(path))
                                        continue;
                        }
                        return 0;
                }
                c = *path++;
        }
}

/*
 * Do we have another file that has the beginning components being a
 * proper superset of the name we're trying to add?
 */
static int has_file_name(struct index_state *istate,
                         const struct cache_entry *ce, int pos, int ok_to_replace)
{
        int retval = 0;
        int len = ce_namelen(ce);
        int stage = ce_stage(ce);
        const char *name = ce->name;

        while (pos < istate->cache_nr) {
                struct cache_entry *p = istate->cache[pos++];

                if (len >= ce_namelen(p))
                        break;
                if (memcmp(name, p->name, len))
                        break;
                if (ce_stage(p) != stage)
                        continue;
                if (p->name[len] != '/')
                        continue;
                if (p->ce_flags & CE_REMOVE)
                        continue;
                retval = -1;
                if (!ok_to_replace)
                        break;
                remove_index_entry_at(istate, --pos);
        }
        return retval;
}

/*
 * Do we have another file with a pathname that is a proper
 * subset of the name we're trying to add?
 */
static int has_dir_name(struct index_state *istate,
                        const struct cache_entry *ce, int pos, int ok_to_replace)
{
        int retval = 0;
        int stage = ce_stage(ce);
        const char *name = ce->name;
        const char *slash = name + ce_namelen(ce);

        for (;;) {
                int len;

                for (;;) {
                        if (*--slash == '/')
                                break;
                        if (slash <= ce->name)
                                return retval;
                }
                len = slash - name;

                pos = index_name_pos(istate, name, create_ce_flags(len, stage));
                if (pos >= 0) {
                        /*
                         * Found one, but not so fast.  This could
                         * be a marker that says "I was here, but
                         * I am being removed".  Such an entry is
                         * not a part of the resulting tree, and
                         * it is Ok to have a directory at the same
                         * path.
                         */
                        if (!(istate->cache[pos]->ce_flags & CE_REMOVE)) {
                                retval = -1;
                                if (!ok_to_replace)
                                        break;
                                remove_index_entry_at(istate, pos);
                                continue;
                        }
                }
                else
                        pos = -pos-1;

                /*
                 * Trivial optimization: if we find an entry that
                 * already matches the sub-directory, then we know
                 * we're ok, and we can exit.
                 */
                while (pos < istate->cache_nr) {
                        struct cache_entry *p = istate->cache[pos];
                        if ((ce_namelen(p) <= len) ||
                            (p->name[len] != '/') ||
                            memcmp(p->name, name, len))
                                break; /* not our subdirectory */
                        if (ce_stage(p) == stage && !(p->ce_flags & CE_REMOVE))
                                /*
                                 * p is at the same stage as our entry, and
                                 * is a subdirectory of what we are looking
                                 * at, so we cannot have conflicts at our
                                 * level or anything shorter.
                                 */
                                return retval;
                        pos++;
                }
        }
        return retval;
}

/* We may be in a situation where we already have path/file and path
 * is being added, or we already have path and path/file is being
 * added.  Either one would result in a nonsense tree that has path
 * twice when git-write-tree tries to write it out.  Prevent it.
 *
 * If ok-to-replace is specified, we remove the conflicting entries
 * from the cache so the caller should recompute the insert position.
 * When this happens, we return non-zero.
 */
static int check_file_directory_conflict(struct index_state *istate,
                                         const struct cache_entry *ce,
                                         int pos, int ok_to_replace)
{
        int retval;

        /*
         * When ce is an "I am going away" entry, we allow it to be added
         */
        if (ce->ce_flags & CE_REMOVE)
                return 0;

        /*
         * We check if the path is a sub-path of a subsequent pathname
         * first, since removing those will not change the position
         * in the array.
         */
        retval = has_file_name(istate, ce, pos, ok_to_replace);

        /*
         * Then check if the path might have a clashing sub-directory
         * before it.
         */
        return retval + has_dir_name(istate, ce, pos, ok_to_replace);
}

static int add_index_entry_with_check(struct index_state *istate, struct cache_entry *ce, int option)
{
        int pos;
        int ok_to_add = option & ADD_CACHE_OK_TO_ADD;
        int ok_to_replace = option & ADD_CACHE_OK_TO_REPLACE;
        int skip_df_check = option & ADD_CACHE_SKIP_DFCHECK;

        cache_tree_invalidate_path(istate->cache_tree, ce->name);
        pos = index_name_pos(istate, ce->name, ce->ce_flags);

        /* existing match? Just replace it. */
        if (pos >= 0) {
                replace_index_entry(istate, pos, ce);
                return 0;
        }
        pos = -pos-1;

        /*
         * Inserting a merged entry ("stage 0") into the index
         * will always replace all non-merged entries..
         */
        if (pos < istate->cache_nr && ce_stage(ce) == 0) {
                while (ce_same_name(istate->cache[pos], ce)) {
                        ok_to_add = 1;
                        if (!remove_index_entry_at(istate, pos))
                                break;
                }
        }

        if (!ok_to_add)
                return -1;
        if (!verify_path(ce->name))
                return -1;

        if (!skip_df_check &&
            check_file_directory_conflict(istate, ce, pos, ok_to_replace)) {
                if (!ok_to_replace)
                        return error("'%s' appears as both a file and as a directory",
                                     ce->name);
                pos = index_name_pos(istate, ce->name, ce->ce_flags);
                pos = -pos-1;
        }
        return pos + 1;
}

int add_index_entry(struct index_state *istate, struct cache_entry *ce, int option)
{
        int pos;

        if (option & ADD_CACHE_JUST_APPEND)
                pos = istate->cache_nr;
        else {
                int ret;
                ret = add_index_entry_with_check(istate, ce, option);
                if (ret <= 0)
                        return ret;
                pos = ret - 1;
        }

        /* Make sure the array is big enough .. */
        if (istate->cache_nr == istate->cache_alloc) {
                istate->cache_alloc = alloc_nr(istate->cache_alloc);
                istate->cache = xrealloc(istate->cache,
                                        istate->cache_alloc * sizeof(struct cache_entry *));
        }

        /* Add it in.. */
        istate->cache_nr++;
        if (istate->cache_nr > pos + 1)
                memmove(istate->cache + pos + 1,
                        istate->cache + pos,
                        (istate->cache_nr - pos - 1) * sizeof(ce));
        set_index_entry(istate, pos, ce);
        istate->cache_changed = 1;
        return 0;
}

/*
 * "refresh" does not calculate a new sha1 file or bring the
 * cache up-to-date for mode/content changes. But what it
 * _does_ do is to "re-match" the stat information of a file
 * with the cache, so that you can refresh the cache for a
 * file that hasn't been changed but where the stat entry is
 * out of date.
 *
 * For example, you'd want to do this after doing a "git-read-tree",
 * to link up the stat cache details with the proper files.
 */
static struct cache_entry *refresh_cache_ent(struct index_state *istate,
                                             struct cache_entry *ce,
                                             unsigned int options, int *err)
{
        struct stat st;
        struct cache_entry *updated;
        int changed, size;
        int ignore_valid = options & CE_MATCH_IGNORE_VALID;

        if (ce_uptodate(ce))
                return ce;

        if (lstat(ce->name, &st) < 0) {
                if (err)
                        *err = errno;
                return NULL;
        }

        changed = ie_match_stat(istate, ce, &st, options);
        if (!changed) {
                /*
                 * The path is unchanged.  If we were told to ignore
                 * valid bit, then we did the actual stat check and
                 * found that the entry is unmodified.  If the entry
                 * is not marked VALID, this is the place to mark it
                 * valid again, under "assume unchanged" mode.
                 */
                if (ignore_valid && assume_unchanged &&
                    !(ce->ce_flags & CE_VALID))
                        ; /* mark this one VALID again */
                else {
                        /*
                         * We do not mark the index itself "modified"
                         * because CE_UPTODATE flag is in-core only;
                         * we are not going to write this change out.
                         */
                        ce_mark_uptodate(ce);
                        return ce;
                }
        }

        if (ie_modified(istate, ce, &st, options)) {
                if (err)
                        *err = EINVAL;
                return NULL;
        }

        size = ce_size(ce);
        updated = xmalloc(size);
        memcpy(updated, ce, size);
        fill_stat_cache_info(updated, &st);
        /*
         * If ignore_valid is not set, we should leave CE_VALID bit
         * alone.  Otherwise, paths marked with --no-assume-unchanged
         * (i.e. things to be edited) will reacquire CE_VALID bit
         * automatically, which is not really what we want.
         */
        if (!ignore_valid && assume_unchanged &&
            !(ce->ce_flags & CE_VALID))
                updated->ce_flags &= ~CE_VALID;

        return updated;
}

int refresh_index(struct index_state *istate, unsigned int flags, const char **pathspec, char *seen)
{
        int i;
        int has_errors = 0;
        int really = (flags & REFRESH_REALLY) != 0;
        int allow_unmerged = (flags & REFRESH_UNMERGED) != 0;
        int quiet = (flags & REFRESH_QUIET) != 0;
        int not_new = (flags & REFRESH_IGNORE_MISSING) != 0;
        unsigned int options = really ? CE_MATCH_IGNORE_VALID : 0;

        for (i = 0; i < istate->cache_nr; i++) {
                struct cache_entry *ce, *new;
                int cache_errno = 0;

                ce = istate->cache[i];
                if (ce_stage(ce)) {
                        while ((i < istate->cache_nr) &&
                               ! strcmp(istate->cache[i]->name, ce->name))
                                i++;
                        i--;
                        if (allow_unmerged)
                                continue;
                        printf("%s: needs merge\n", ce->name);
                        has_errors = 1;
                        continue;
                }

                if (pathspec && !match_pathspec(pathspec, ce->name, strlen(ce->name), 0, seen))
                        continue;

                new = refresh_cache_ent(istate, ce, options, &cache_errno);
                if (new == ce)
                        continue;
                if (!new) {
                        if (not_new && cache_errno == ENOENT)
                                continue;
                        if (really && cache_errno == EINVAL) {
                                /* If we are doing --really-refresh that
                                 * means the index is not valid anymore.
                                 */
                                ce->ce_flags &= ~CE_VALID;
                                istate->cache_changed = 1;
                        }
                        if (quiet)
                                continue;
                        printf("%s: needs update\n", ce->name);
                        has_errors = 1;
                        continue;
                }

                replace_index_entry(istate, i, new);
        }
        return has_errors;
}

struct cache_entry *refresh_cache_entry(struct cache_entry *ce, int really)
{
        return refresh_cache_ent(&the_index, ce, really, NULL);
}

static int verify_hdr(struct cache_header *hdr, unsigned long size)
{
        SHA_CTX c;
        unsigned char sha1[20];

        if (hdr->hdr_signature != htonl(CACHE_SIGNATURE))
                return error("bad signature");
        if (hdr->hdr_version != htonl(2))
                return error("bad index version");
        SHA1_Init(&c);
        SHA1_Update(&c, hdr, size - 20);
        SHA1_Final(sha1, &c);
        if (hashcmp(sha1, (unsigned char *)hdr + size - 20))
                return error("bad index file sha1 signature");
        return 0;
}

static int read_index_extension(struct index_state *istate,
                                const char *ext, void *data, unsigned long sz)
{
        switch (CACHE_EXT(ext)) {
        case CACHE_EXT_TREE:
                istate->cache_tree = cache_tree_read(data, sz);
                break;
        default:
                if (*ext < 'A' || 'Z' < *ext)
                        return error("index uses %.4s extension, which we do not understand",
                                     ext);
                fprintf(stderr, "ignoring %.4s extension\n", ext);
                break;
        }
        return 0;
}

int read_index(struct index_state *istate)
{
        return read_index_from(istate, get_index_file());
}

static void convert_from_disk(struct ondisk_cache_entry *ondisk, struct cache_entry *ce)
{
        size_t len;

        ce->ce_ctime = ntohl(ondisk->ctime.sec);
        ce->ce_mtime = ntohl(ondisk->mtime.sec);
        ce->ce_dev   = ntohl(ondisk->dev);
        ce->ce_ino   = ntohl(ondisk->ino);
        ce->ce_mode  = ntohl(ondisk->mode);
        ce->ce_uid   = ntohl(ondisk->uid);
        ce->ce_gid   = ntohl(ondisk->gid);
        ce->ce_size  = ntohl(ondisk->size);
        /* On-disk flags are just 16 bits */
        ce->ce_flags = ntohs(ondisk->flags);
        hashcpy(ce->sha1, ondisk->sha1);

        len = ce->ce_flags & CE_NAMEMASK;
        if (len == CE_NAMEMASK)
                len = strlen(ondisk->name);
        /*
         * NEEDSWORK: If the original index is crafted, this copy could
         * go unchecked.
         */
        memcpy(ce->name, ondisk->name, len + 1);
}

static inline size_t estimate_cache_size(size_t ondisk_size, unsigned int entries)
{
        long per_entry;

        per_entry = sizeof(struct cache_entry) - sizeof(struct ondisk_cache_entry);

        /*
         * Alignment can cause differences. This should be "alignof", but
         * since that's a gcc'ism, just use the size of a pointer.
         */
        per_entry += sizeof(void *);
        return ondisk_size + entries*per_entry;
}

/* remember to discard_cache() before reading a different cache! */
int read_index_from(struct index_state *istate, const char *path)
{
        int fd, i;
        struct stat st;
        unsigned long src_offset, dst_offset;
        struct cache_header *hdr;
        void *mmap;
        size_t mmap_size;

        errno = EBUSY;
        if (istate->alloc)
                return istate->cache_nr;

        errno = ENOENT;
        istate->timestamp = 0;
        fd = open(path, O_RDONLY);
        if (fd < 0) {
                if (errno == ENOENT)
                        return 0;
                die("index file open failed (%s)", strerror(errno));
        }

        if (fstat(fd, &st))
                die("cannot stat the open index (%s)", strerror(errno));

        errno = EINVAL;
        mmap_size = xsize_t(st.st_size);
        if (mmap_size < sizeof(struct cache_header) + 20)
                die("index file smaller than expected");

        mmap = xmmap(NULL, mmap_size, PROT_READ | PROT_WRITE, MAP_PRIVATE, fd, 0);
        close(fd);
        if (mmap == MAP_FAILED)
                die("unable to map index file");

        hdr = mmap;
        if (verify_hdr(hdr, mmap_size) < 0)
                goto unmap;

        istate->cache_nr = ntohl(hdr->hdr_entries);
        istate->cache_alloc = alloc_nr(istate->cache_nr);
        istate->cache = xcalloc(istate->cache_alloc, sizeof(struct cache_entry *));

        /*
         * The disk format is actually larger than the in-memory format,
         * due to space for nsec etc, so even though the in-memory one
         * has room for a few  more flags, we can allocate using the same
         * index size
         */
        istate->alloc = xmalloc(estimate_cache_size(mmap_size, istate->cache_nr));

        src_offset = sizeof(*hdr);
        dst_offset = 0;
        for (i = 0; i < istate->cache_nr; i++) {
                struct ondisk_cache_entry *disk_ce;
                struct cache_entry *ce;

                disk_ce = (struct ondisk_cache_entry *)((char *)mmap + src_offset);
                ce = (struct cache_entry *)((char *)istate->alloc + dst_offset);
                convert_from_disk(disk_ce, ce);
                set_index_entry(istate, i, ce);

                src_offset += ondisk_ce_size(ce);
                dst_offset += ce_size(ce);
        }
        istate->timestamp = st.st_mtime;
        while (src_offset <= mmap_size - 20 - 8) {
                /* After an array of active_nr index entries,
                 * there can be arbitrary number of extended
                 * sections, each of which is prefixed with
                 * extension name (4-byte) and section length
                 * in 4-byte network byte order.
                 */
                unsigned long extsize;
                memcpy(&extsize, (char *)mmap + src_offset + 4, 4);
                extsize = ntohl(extsize);
                if (read_index_extension(istate,
                                         (const char *) mmap + src_offset,
                                         (char *) mmap + src_offset + 8,
                                         extsize) < 0)
                        goto unmap;
                src_offset += 8;
                src_offset += extsize;
        }
        munmap(mmap, mmap_size);
        return istate->cache_nr;

unmap:
        munmap(mmap, mmap_size);
        errno = EINVAL;
        die("index file corrupt");
}

int discard_index(struct index_state *istate)
{
        istate->cache_nr = 0;
        istate->cache_changed = 0;
        istate->timestamp = 0;
        free_hash(&istate->name_hash);
        cache_tree_free(&(istate->cache_tree));
        free(istate->alloc);
        istate->alloc = NULL;

        /* no need to throw away allocated active_cache */
        return 0;
}

int unmerged_index(const struct index_state *istate)
{
        int i;
        for (i = 0; i < istate->cache_nr; i++) {
                if (ce_stage(istate->cache[i]))
                        return 1;
        }
        return 0;
}

#define WRITE_BUFFER_SIZE 8192
static unsigned char write_buffer[WRITE_BUFFER_SIZE];
static unsigned long write_buffer_len;

static int ce_write_flush(SHA_CTX *context, int fd)
{
        unsigned int buffered = write_buffer_len;
        if (buffered) {
                SHA1_Update(context, write_buffer, buffered);
                if (write_in_full(fd, write_buffer, buffered) != buffered)
                        return -1;
                write_buffer_len = 0;
        }
        return 0;
}

static int ce_write(SHA_CTX *context, int fd, void *data, unsigned int len)
{
        while (len) {
                unsigned int buffered = write_buffer_len;
                unsigned int partial = WRITE_BUFFER_SIZE - buffered;
                if (partial > len)
                        partial = len;
                memcpy(write_buffer + buffered, data, partial);
                buffered += partial;
                if (buffered == WRITE_BUFFER_SIZE) {
                        write_buffer_len = buffered;
                        if (ce_write_flush(context, fd))
                                return -1;
                        buffered = 0;
                }
                write_buffer_len = buffered;
                len -= partial;
                data = (char *) data + partial;
        }
        return 0;
}

static int write_index_ext_header(SHA_CTX *context, int fd,
                                  unsigned int ext, unsigned int sz)
{
        ext = htonl(ext);
        sz = htonl(sz);
        return ((ce_write(context, fd, &ext, 4) < 0) ||
                (ce_write(context, fd, &sz, 4) < 0)) ? -1 : 0;
}

static int ce_flush(SHA_CTX *context, int fd)
{
        unsigned int left = write_buffer_len;

        if (left) {
                write_buffer_len = 0;
                SHA1_Update(context, write_buffer, left);
        }

        /* Flush first if not enough space for SHA1 signature */
        if (left + 20 > WRITE_BUFFER_SIZE) {
                if (write_in_full(fd, write_buffer, left) != left)
                        return -1;
                left = 0;
        }

        /* Append the SHA1 signature at the end */
        SHA1_Final(write_buffer + left, context);
        left += 20;
        return (write_in_full(fd, write_buffer, left) != left) ? -1 : 0;
}

static void ce_smudge_racily_clean_entry(struct cache_entry *ce)
{
        /*
         * The only thing we care about in this function is to smudge the
         * falsely clean entry due to touch-update-touch race, so we leave
         * everything else as they are.  We are called for entries whose
         * ce_mtime match the index file mtime.
         */
        struct stat st;

        if (lstat(ce->name, &st) < 0)
                return;
        if (ce_match_stat_basic(ce, &st))
                return;
        if (ce_modified_check_fs(ce, &st)) {
                /* This is "racily clean"; smudge it.  Note that this
                 * is a tricky code.  At first glance, it may appear
                 * that it can break with this sequence:
                 *
                 * $ echo xyzzy >frotz
                 * $ git-update-index --add frotz
                 * $ : >frotz
                 * $ sleep 3
                 * $ echo filfre >nitfol
                 * $ git-update-index --add nitfol
                 *
                 * but it does not.  When the second update-index runs,
                 * it notices that the entry "frotz" has the same timestamp
                 * as index, and if we were to smudge it by resetting its
                 * size to zero here, then the object name recorded
                 * in index is the 6-byte file but the cached stat information
                 * becomes zero --- which would then match what we would
                 * obtain from the filesystem next time we stat("frotz").
                 *
                 * However, the second update-index, before calling
                 * this function, notices that the cached size is 6
                 * bytes and what is on the filesystem is an empty
                 * file, and never calls us, so the cached size information
                 * for "frotz" stays 6 which does not match the filesystem.
                 */
                ce->ce_size = 0;
        }
}

static int ce_write_entry(SHA_CTX *c, int fd, struct cache_entry *ce)
{
        int size = ondisk_ce_size(ce);
        struct ondisk_cache_entry *ondisk = xcalloc(1, size);

        ondisk->ctime.sec = htonl(ce->ce_ctime);
        ondisk->ctime.nsec = 0;
        ondisk->mtime.sec = htonl(ce->ce_mtime);
        ondisk->mtime.nsec = 0;
        ondisk->dev  = htonl(ce->ce_dev);
        ondisk->ino  = htonl(ce->ce_ino);
        ondisk->mode = htonl(ce->ce_mode);
        ondisk->uid  = htonl(ce->ce_uid);
        ondisk->gid  = htonl(ce->ce_gid);
        ondisk->size = htonl(ce->ce_size);
        hashcpy(ondisk->sha1, ce->sha1);
        ondisk->flags = htons(ce->ce_flags);
        memcpy(ondisk->name, ce->name, ce_namelen(ce));

        return ce_write(c, fd, ondisk, size);
}

int write_index(const struct index_state *istate, int newfd)
{
        SHA_CTX c;
        struct cache_header hdr;
        int i, err, removed;
        struct cache_entry **cache = istate->cache;
        int entries = istate->cache_nr;

        for (i = removed = 0; i < entries; i++)
                if (cache[i]->ce_flags & CE_REMOVE)
                        removed++;

        hdr.hdr_signature = htonl(CACHE_SIGNATURE);
        hdr.hdr_version = htonl(2);
        hdr.hdr_entries = htonl(entries - removed);

        SHA1_Init(&c);
        if (ce_write(&c, newfd, &hdr, sizeof(hdr)) < 0)
                return -1;

        for (i = 0; i < entries; i++) {
                struct cache_entry *ce = cache[i];
                if (ce->ce_flags & CE_REMOVE)
                        continue;
                if (is_racy_timestamp(istate, ce))
                        ce_smudge_racily_clean_entry(ce);
                if (ce_write_entry(&c, newfd, ce) < 0)
                        return -1;
        }

        /* Write extension data here */
        if (istate->cache_tree) {
                struct strbuf sb;

                strbuf_init(&sb, 0);
                cache_tree_write(&sb, istate->cache_tree);
                err = write_index_ext_header(&c, newfd, CACHE_EXT_TREE, sb.len) < 0
                        || ce_write(&c, newfd, sb.buf, sb.len) < 0;
                strbuf_release(&sb);
                if (err)
                        return -1;
        }
        return ce_flush(&c, newfd);
}