CE_REMOVE'd entries are removed here because only parts of the code
base (unpack_trees in fact) test this bit when they look for the
presence of an entry. Leaving them may confuse the code ignores this
bit and expects to see a real entry.

Signed-off-by: Nguyễn Thái Ngọc Duy <pclo...@gmail.com>
---
 read-cache.c  |  2 --
 split-index.c | 84 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++--
 split-index.h |  2 ++
 3 files changed, 84 insertions(+), 4 deletions(-)

diff --git a/read-cache.c b/read-cache.c
index 7966fb7..1a7ef7f 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -1569,8 +1569,6 @@ int read_index_from(struct index_state *istate, const 
char *path)
 
        if (is_null_sha1(split_index->base_sha1))
                return ret;
-       if (istate->cache_nr)
-               die("index in split-index mode must contain no entries");
 
        if (split_index->base)
                discard_index(split_index->base);
diff --git a/split-index.c b/split-index.c
index 5708807..b03a250 100644
--- a/split-index.c
+++ b/split-index.c
@@ -16,13 +16,27 @@ int read_link_extension(struct index_state *istate,
 {
        const unsigned char *data = data_;
        struct split_index *si;
+       int ret;
+
        if (sz < 20)
                return error("corrupt link extension (too short)");
        si = init_split_index(istate);
        hashcpy(si->base_sha1, data);
        data += 20;
        sz -= 20;
-       if (sz)
+       if (!sz)
+               return 0;
+       si->delete_bitmap = ewah_new();
+       ret = ewah_read_mmap(si->delete_bitmap, data, sz);
+       if (ret < 0)
+               return error("corrupt delete bitmap in link extension");
+       data += ret;
+       sz -= ret;
+       si->replace_bitmap = ewah_new();
+       ret = ewah_read_mmap(si->replace_bitmap, data, sz);
+       if (ret < 0)
+               return error("corrupt replace bitmap in link extension");
+       if (ret != sz)
                return error("garbage at the end of link extension");
        return 0;
 }
@@ -60,15 +74,81 @@ static void mark_base_index_entries(struct index_state 
*base)
                base->cache[i]->index = i + 1;
 }
 
+static void mark_entry_for_delete(size_t pos, void *data)
+{
+       struct index_state *istate = data;
+       if (pos >= istate->cache_nr)
+               die("position for delete %d exceeds base index size %d",
+                   (int)pos, istate->cache_nr);
+       istate->cache[pos]->ce_flags |= CE_REMOVE;
+       istate->split_index->nr_deletions = 1;
+}
+
+static void replace_entry(size_t pos, void *data)
+{
+       struct index_state *istate = data;
+       struct split_index *si = istate->split_index;
+       struct cache_entry *dst, *src;
+       if (pos >= istate->cache_nr)
+               die("position for replacement %d exceeds base index size %d",
+                   (int)pos, istate->cache_nr);
+       if (si->nr_replacements >= si->saved_cache_nr)
+               die("too many replacements (%d vs %d)",
+                   si->nr_replacements, si->saved_cache_nr);
+       dst = istate->cache[pos];
+       if (dst->ce_flags & CE_REMOVE)
+               die("entry %d is marked as both replaced and deleted",
+                   (int)pos);
+       src = si->saved_cache[si->nr_replacements];
+       src->index = pos + 1;
+       src->ce_flags |= CE_UPDATE_IN_BASE;
+       free(dst);
+       dst = src;
+       si->nr_replacements++;
+}
+
 void merge_base_index(struct index_state *istate)
 {
        struct split_index *si = istate->split_index;
+       unsigned int i;
 
        mark_base_index_entries(si->base);
-       istate->cache_nr = si->base->cache_nr;
+
+       si->saved_cache     = istate->cache;
+       si->saved_cache_nr  = istate->cache_nr;
+       istate->cache_nr    = si->base->cache_nr;
+       istate->cache       = NULL;
+       istate->cache_alloc = 0;
        ALLOC_GROW(istate->cache, istate->cache_nr, istate->cache_alloc);
        memcpy(istate->cache, si->base->cache,
               sizeof(*istate->cache) * istate->cache_nr);
+
+       si->nr_deletions = 0;
+       si->nr_replacements = 0;
+       ewah_each_bit(si->replace_bitmap, replace_entry, istate);
+       ewah_each_bit(si->delete_bitmap, mark_entry_for_delete, istate);
+       if (si->nr_deletions)
+               remove_marked_cache_entries(istate);
+
+       for (i = si->nr_replacements; i < si->saved_cache_nr; i++) {
+               add_index_entry(istate, si->saved_cache[i],
+                               ADD_CACHE_OK_TO_ADD |
+                               /*
+                                * we may have to replay what
+                                * merge-recursive.c:update_stages()
+                                * does, which has this flag on
+                                */
+                               ADD_CACHE_SKIP_DFCHECK);
+               si->saved_cache[i] = NULL;
+       }
+
+       ewah_free(si->delete_bitmap);
+       ewah_free(si->replace_bitmap);
+       free(si->saved_cache);
+       si->delete_bitmap  = NULL;
+       si->replace_bitmap = NULL;
+       si->saved_cache    = NULL;
+       si->saved_cache_nr = 0;
 }
 
 void prepare_to_write_split_index(struct index_state *istate)
diff --git a/split-index.h b/split-index.h
index 53b778f..c1324f5 100644
--- a/split-index.h
+++ b/split-index.h
@@ -12,6 +12,8 @@ struct split_index {
        struct ewah_bitmap *replace_bitmap;
        struct cache_entry **saved_cache;
        unsigned int saved_cache_nr;
+       unsigned int nr_deletions;
+       unsigned int nr_replacements;
        int refcount;
 };
 
-- 
1.9.1.346.ga2b5940

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