read-cache: mark updated entries for split index

The large part of this patch just follows CE_ENTRY_CHANGED
marks. replace_index_entry() is updated to update
split_index->base->cache[] as well so base->cache[] does not reference
to a freed entry.

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

builtin/update-index.c

@@ -55,6 +55,7 @@ static int mark_ce_flags(const char *path, int flag, int mark)
 			active_cache[pos]->ce_flags |= flag;
 		else
 			active_cache[pos]->ce_flags &= ~flag;
+		active_cache[pos]->ce_flags |= CE_UPDATE_IN_BASE;
 		cache_tree_invalidate_path(&the_index, path);
 		active_cache_changed |= CE_ENTRY_CHANGED;
 		return 0;
@@ -268,6 +269,7 @@ static void chmod_path(int flip, const char *path)
 		goto fail;
 	}
 	cache_tree_invalidate_path(&the_index, path);
+	ce->ce_flags |= CE_UPDATE_IN_BASE;
 	active_cache_changed |= CE_ENTRY_CHANGED;
 	report("chmod %cx '%s'", flip, path);
 	return;

cache.h

@@ -169,6 +169,8 @@ struct cache_entry {
 /* used to temporarily mark paths matched by pathspecs */
 #define CE_MATCHED           (1 << 26)
 
+#define CE_UPDATE_IN_BASE    (1 << 27)
+
 /*
  * Extended on-disk flags
  */

entry.c

@@ -214,6 +214,7 @@ static int write_entry(struct cache_entry *ce,
 		if (!fstat_done)
 			lstat(ce->name, &st);
 		fill_stat_cache_info(ce, &st);
+		ce->ce_flags |= CE_UPDATE_IN_BASE;
 		state->istate->cache_changed |= CE_ENTRY_CHANGED;
 	}
 	return 0;

read-cache.c

@@ -39,7 +39,7 @@ static struct cache_entry *refresh_cache_entry(struct cache_entry *ce,
 
 /* changes that can be kept in $GIT_DIR/index (basically all extensions) */
 #define EXTMASK (RESOLVE_UNDO_CHANGED | CACHE_TREE_CHANGED | \
-		 CE_ENTRY_ADDED | CE_ENTRY_REMOVED)
+		 CE_ENTRY_ADDED | CE_ENTRY_REMOVED | CE_ENTRY_CHANGED)
 
 struct index_state the_index;
 static const char *alternate_index_output;
@@ -54,9 +54,11 @@ static void replace_index_entry(struct index_state *istate, int nr, struct cache
 {
 	struct cache_entry *old = istate->cache[nr];
 
+	replace_index_entry_in_base(istate, old, ce);
 	remove_name_hash(istate, old);
 	free(old);
 	set_index_entry(istate, nr, ce);
+	ce->ce_flags |= CE_UPDATE_IN_BASE;
 	istate->cache_changed |= CE_ENTRY_CHANGED;
 }
 
@@ -1192,6 +1194,7 @@ int refresh_index(struct index_state *istate, unsigned int flags,
 				 * means the index is not valid anymore.
 				 */
 				ce->ce_flags &= ~CE_VALID;
+				ce->ce_flags |= CE_UPDATE_IN_BASE;
 				istate->cache_changed |= CE_ENTRY_CHANGED;
 			}
 			if (quiet)

split-index.c

@@ -100,3 +100,18 @@ void save_or_free_index_entry(struct index_state *istate, struct cache_entry *ce
 	else
 		free(ce);
 }
+
+void replace_index_entry_in_base(struct index_state *istate,
+				 struct cache_entry *old,
+				 struct cache_entry *new)
+{
+	if (old->index &&
+	    istate->split_index &&
+	    istate->split_index->base &&
+	    old->index <= istate->split_index->base->cache_nr) {
+		new->index = old->index;
+		if (old != istate->split_index->base->cache[new->index - 1])
+			free(istate->split_index->base->cache[new->index - 1]);
+		istate->split_index->base->cache[new->index - 1] = new;
+	}
+}

split-index.h

@@ -13,6 +13,9 @@ struct split_index {
 
 struct split_index *init_split_index(struct index_state *istate);
 void save_or_free_index_entry(struct index_state *istate, struct cache_entry *ce);
+void replace_index_entry_in_base(struct index_state *istate,
+				 struct cache_entry *old,
+				 struct cache_entry *new);
 int read_link_extension(struct index_state *istate,
 			const void *data, unsigned long sz);
 int write_link_extension(struct strbuf *sb,

unpack-trees.c

@@ -257,8 +257,10 @@ static int apply_sparse_checkout(struct index_state *istate,
 		ce->ce_flags |= CE_SKIP_WORKTREE;
 	else
 		ce->ce_flags &= ~CE_SKIP_WORKTREE;
-	if (was_skip_worktree != ce_skip_worktree(ce))
+	if (was_skip_worktree != ce_skip_worktree(ce)) {
+		ce->ce_flags |= CE_UPDATE_IN_BASE;
 		istate->cache_changed |= CE_ENTRY_CHANGED;
+	}
 
 	/*
 	 * if (!was_skip_worktree && !ce_skip_worktree()) {