unpack-trees: convert clear_ce_flags* to avoid the_index

Prior to fba92be8f7, this code implicitly (and incorrectly) assumes
the_index when running the exclude machinery. fba92be8f7 helps show
this problem clearer because unpack-trees operation is supposed to
work on whatever index the caller specifies... not specifically
the_index.

Update the code to use "istate" argument that's originally from
mark_new_skip_worktree(). From the call sites, both in unpack_trees(),
you can see that this function works on two separate indexes:
o->src_index and o->result. The second mark_new_skip_worktree() so far
has incorecctly applied exclude rules on o->src_index instead of
o->result. It's unclear what is the consequences of this, but it's
definitely wrong.

[1] fba92be8f7 (dir: convert is_excluded_from_list to take an index -
    2017-05-05)

Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

unpack-trees.c

@@ -1092,13 +1092,15 @@ static int unpack_callback(int n, unsigned long mask, unsigned long dirmask, str
 	return mask;
 }
 
-static int clear_ce_flags_1(struct cache_entry **cache, int nr,
+static int clear_ce_flags_1(struct index_state *istate,
+			    struct cache_entry **cache, int nr,
 			    struct strbuf *prefix,
 			    int select_mask, int clear_mask,
 			    struct exclude_list *el, int defval);
 
 /* Whole directory matching */
-static int clear_ce_flags_dir(struct cache_entry **cache, int nr,
+static int clear_ce_flags_dir(struct index_state *istate,
+			      struct cache_entry **cache, int nr,
 			      struct strbuf *prefix,
 			      char *basename,
 			      int select_mask, int clear_mask,
@@ -1107,7 +1109,7 @@ static int clear_ce_flags_dir(struct cache_entry **cache, int nr,
 	struct cache_entry **cache_end;
 	int dtype = DT_DIR;
 	int ret = is_excluded_from_list(prefix->buf, prefix->len,
-					basename, &dtype, el, &the_index);
+					basename, &dtype, el, istate);
 	int rc;
 
 	strbuf_addch(prefix, '/');
@@ -1129,7 +1131,7 @@ static int clear_ce_flags_dir(struct cache_entry **cache, int nr,
 	 * calling clear_ce_flags_1(). That function will call
 	 * the expensive is_excluded_from_list() on every entry.
 	 */
-	rc = clear_ce_flags_1(cache, cache_end - cache,
+	rc = clear_ce_flags_1(istate, cache, cache_end - cache,
 			      prefix,
 			      select_mask, clear_mask,
 			      el, ret);
@@ -1152,7 +1154,8 @@ static int clear_ce_flags_dir(struct cache_entry **cache, int nr,
  *   cache[0]->name[0..(prefix_len-1)]
  * Top level path has prefix_len zero.
  */
-static int clear_ce_flags_1(struct cache_entry **cache, int nr,
+static int clear_ce_flags_1(struct index_state *istate,
+			    struct cache_entry **cache, int nr,
 			    struct strbuf *prefix,
 			    int select_mask, int clear_mask,
 			    struct exclude_list *el, int defval)
@@ -1186,7 +1189,7 @@ static int clear_ce_flags_1(struct cache_entry **cache, int nr,
 			len = slash - name;
 			strbuf_add(prefix, name, len);
 
-			processed = clear_ce_flags_dir(cache, cache_end - cache,
+			processed = clear_ce_flags_dir(istate, cache, cache_end - cache,
 						       prefix,
 						       prefix->buf + prefix->len - len,
 						       select_mask, clear_mask,
@@ -1200,7 +1203,7 @@ static int clear_ce_flags_1(struct cache_entry **cache, int nr,
 			}
 
 			strbuf_addch(prefix, '/');
-			cache += clear_ce_flags_1(cache, cache_end - cache,
+			cache += clear_ce_flags_1(istate, cache, cache_end - cache,
 						  prefix,
 						  select_mask, clear_mask, el, defval);
 			strbuf_setlen(prefix, prefix->len - len - 1);
@@ -1210,7 +1213,7 @@ static int clear_ce_flags_1(struct cache_entry **cache, int nr,
 		/* Non-directory */
 		dtype = ce_to_dtype(ce);
 		ret = is_excluded_from_list(ce->name, ce_namelen(ce),
-					    name, &dtype, el, &the_index);
+					    name, &dtype, el, istate);
 		if (ret < 0)
 			ret = defval;
 		if (ret > 0)
@@ -1220,7 +1223,7 @@ static int clear_ce_flags_1(struct cache_entry **cache, int nr,
 	return nr - (cache_end - cache);
 }
 
-static int clear_ce_flags(struct cache_entry **cache, int nr,
+static int clear_ce_flags(struct index_state *istate,
 			  int select_mask, int clear_mask,
 			  struct exclude_list *el)
 {
@@ -1228,7 +1231,9 @@ static int clear_ce_flags(struct cache_entry **cache, int nr,
 
 	strbuf_reset(&prefix);
 
-	return clear_ce_flags_1(cache, nr,
+	return clear_ce_flags_1(istate,
+				istate->cache,
+				istate->cache_nr,
 				&prefix,
 				select_mask, clear_mask,
 				el, 0);
@@ -1263,7 +1268,7 @@ static void mark_new_skip_worktree(struct exclude_list *el,
 	 * 2. Widen worktree according to sparse-checkout file.
 	 * Matched entries will have skip_wt_flag cleared (i.e. "in")
 	 */
-	clear_ce_flags(istate->cache, istate->cache_nr, select_flag, skip_wt_flag, el);
+	clear_ce_flags(istate, select_flag, skip_wt_flag, el);
 }
 
 static int verify_absent(const struct cache_entry *,