if (*ptr == '/') {
                                struct cache_entry *foundce;
                                ++ptr;
-                               foundce = index_name_exists(istate, ce->name, ptr - ce->name, ignore_case);
+                               foundce = index_dir_exists(istate, ce->name, ptr - ce->name - 1);
                                if (foundce) {
                                        memcpy((void *)startPtr, foundce->name + (startPtr - ce->name), ptr - startPtr);
                                        startPtr = ptr;
                }
        }
 
-       alias = index_name_exists(istate, ce->name, ce_namelen(ce), ignore_case);
+       alias = index_file_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);
        printf(fmt, name);
 }
 
-int refresh_index(struct index_state *istate, unsigned int flags, const char **pathspec,
+int refresh_index(struct index_state *istate, unsigned int flags,
+                 const struct pathspec *pathspec,
                  char *seen, const char *header_msg)
 {
        int i;
                        continue;
 
                if (pathspec &&
-                   !match_pathspec(pathspec, ce->name, ce_namelen(ce), 0, seen))
+                   !match_pathspec_depth(pathspec, ce->name, ce_namelen(ce), 0, seen))
                        filtered = 1;
 
                if (ce_stage(ce)) {
 struct ondisk_cache_entry {
        struct cache_time ctime;
        struct cache_time mtime;
-       unsigned int dev;
-       unsigned int ino;
-       unsigned int mode;
-       unsigned int uid;
-       unsigned int gid;
-       unsigned int size;
+       uint32_t dev;
+       uint32_t ino;
+       uint32_t mode;
+       uint32_t uid;
+       uint32_t gid;
+       uint32_t size;
        unsigned char sha1[20];
-       unsigned short flags;
+       uint16_t flags;
        char name[FLEX_ARRAY]; /* more */
 };
 
 struct ondisk_cache_entry_extended {
        struct cache_time ctime;
        struct cache_time mtime;
-       unsigned int dev;
-       unsigned int ino;
-       unsigned int mode;
-       unsigned int uid;
-       unsigned int gid;
-       unsigned int size;
+       uint32_t dev;
+       uint32_t ino;
+       uint32_t mode;
+       uint32_t uid;
+       uint32_t gid;
+       uint32_t size;
        unsigned char sha1[20];
-       unsigned short flags;
-       unsigned short flags2;
+       uint16_t flags;
+       uint16_t flags2;
        char name[FLEX_ARRAY]; /* more */
 };
 
                        continue;
                if (!ce_uptodate(ce) && is_racy_timestamp(istate, ce))
                        ce_smudge_racily_clean_entry(ce);
-               if (is_null_sha1(ce->sha1))
-                       return error("cache entry has null sha1: %s", ce->name);
+               if (is_null_sha1(ce->sha1)) {
+                       static const char msg[] = "cache entry has null sha1: %s";
+                       static int allow = -1;
+
+                       if (allow < 0)
+                               allow = git_env_bool("GIT_ALLOW_NULL_SHA1", 0);
+                       if (allow)
+                               warning(msg, ce->name);
+                       else
+                               return error(msg, ce->name);
+               }
                if (ce_write_entry(&c, newfd, ce, previous_name) < 0)
                        return -1;
        }