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 <pclo...@gmail.com>
---
 builtin/update-index.c |  2 ++
 cache.h                |  2 ++
 entry.c                |  1 +
 read-cache.c           |  5 ++++-
 split-index.c          | 15 +++++++++++++++
 split-index.h          |  3 +++
 unpack-trees.c         |  4 +++-
 7 files changed, 30 insertions(+), 2 deletions(-)

diff --git a/builtin/update-index.c b/builtin/update-index.c
index fa3c441..f7a19c4 100644
--- a/builtin/update-index.c
+++ b/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;
diff --git a/cache.h b/cache.h
index 47fe374..295bf9d 100644
--- a/cache.h
+++ b/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
  */
diff --git a/entry.c b/entry.c
index d913c1d..1eda8e9 100644
--- a/entry.c
+++ b/entry.c
@@ -214,6 +214,7 @@ finish:
                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;
diff --git a/read-cache.c b/read-cache.c
index c437585..7966fb7 100644
--- a/read-cache.c
+++ b/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)
diff --git a/split-index.c b/split-index.c
index 2bb5d55..b36c73b 100644
--- a/split-index.c
+++ b/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;
+       }
+}
diff --git a/split-index.h b/split-index.h
index 5302118..812e510 100644
--- a/split-index.h
+++ b/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,
diff --git a/unpack-trees.c b/unpack-trees.c
index a941f7c..4a9cdf2 100644
--- a/unpack-trees.c
+++ b/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()) {
-- 
1.9.1.346.ga2b5940

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