A filter line in a request to upload-pack filters out objects regardless
of whether they are directly referenced by a "want" line or not. This
means that cloning with "--filter=blob:none" (or another filter that
excludes blobs) from a repository with at least one ref pointing to a
blob (for example, the Git repository itself) results in output like the
following:

    error: missing object referenced by 'refs/tags/junio-gpg-pub'

and if that particular blob is not referenced by a fetched tree, the
resulting clone fails fsck because there is no object from the remote to
vouch that the missing object is a promisor object.

Update both the protocol and the upload-pack implementation to include
all explicitly specified "want" objects in the packfile regardless of
the filter specification.

Signed-off-by: Jonathan Tan <jonathanta...@google.com>
---
 Documentation/technical/pack-protocol.txt |  4 +++-
 list-objects.c                            |  6 +++---
 object.h                                  |  2 +-
 revision.c                                |  1 +
 revision.h                                |  3 ++-
 t/t5317-pack-objects-filter-objects.sh    | 16 ++++++++++++++++
 t/t5616-partial-clone.sh                  | 16 ++++++++++++++++
 7 files changed, 42 insertions(+), 6 deletions(-)

diff --git a/Documentation/technical/pack-protocol.txt 
b/Documentation/technical/pack-protocol.txt
index 7fee6b780a..508a344cf1 100644
--- a/Documentation/technical/pack-protocol.txt
+++ b/Documentation/technical/pack-protocol.txt
@@ -284,7 +284,9 @@ information is sent back to the client in the next step.
 The client can optionally request that pack-objects omit various
 objects from the packfile using one of several filtering techniques.
 These are intended for use with partial clone and partial fetch
-operations.  See `rev-list` for possible "filter-spec" values.
+operations. An object that does not meet a filter-spec value is
+omitted unless explicitly requested in a 'want' line. See `rev-list`
+for possible filter-spec values.
 
 Once all the 'want's and 'shallow's (and optional 'deepen') are
 transferred, clients MUST send a flush-pkt, to tell the server side
diff --git a/list-objects.c b/list-objects.c
index 3eec510357..be4118889a 100644
--- a/list-objects.c
+++ b/list-objects.c
@@ -47,7 +47,7 @@ static void process_blob(struct rev_info *revs,
 
        pathlen = path->len;
        strbuf_addstr(path, name);
-       if (filter_fn)
+       if (!(obj->flags & USER_GIVEN) && filter_fn)
                r = filter_fn(LOFS_BLOB, obj,
                              path->buf, &path->buf[pathlen],
                              filter_data);
@@ -132,7 +132,7 @@ static void process_tree(struct rev_info *revs,
        }
 
        strbuf_addstr(base, name);
-       if (filter_fn)
+       if (!(obj->flags & USER_GIVEN) && filter_fn)
                r = filter_fn(LOFS_BEGIN_TREE, obj,
                              base->buf, &base->buf[baselen],
                              filter_data);
@@ -171,7 +171,7 @@ static void process_tree(struct rev_info *revs,
                                     cb_data, filter_fn, filter_data);
        }
 
-       if (filter_fn) {
+       if (!(obj->flags & USER_GIVEN) && filter_fn) {
                r = filter_fn(LOFS_END_TREE, obj,
                              base->buf, &base->buf[baselen],
                              filter_data);
diff --git a/object.h b/object.h
index 5c13955000..cf8da6ba83 100644
--- a/object.h
+++ b/object.h
@@ -27,7 +27,7 @@ struct object_array {
 
 /*
  * object flag allocation:
- * revision.h:               0---------10                                26
+ * revision.h:               0---------10                              2526
  * fetch-pack.c:             0----5
  * walker.c:                 0-2
  * upload-pack.c:                4       11----------------19
diff --git a/revision.c b/revision.c
index 40fd91ff2b..1b37da988d 100644
--- a/revision.c
+++ b/revision.c
@@ -172,6 +172,7 @@ static void add_pending_object_with_path(struct rev_info 
*revs,
                strbuf_release(&buf);
                return; /* do not add the commit itself */
        }
+       obj->flags |= USER_GIVEN;
        add_object_array_with_path(obj, name, &revs->pending, mode, path);
 }
 
diff --git a/revision.h b/revision.h
index b8c47b98e2..dc8f96366e 100644
--- a/revision.h
+++ b/revision.h
@@ -19,8 +19,9 @@
 #define SYMMETRIC_LEFT (1u<<8)
 #define PATCHSAME      (1u<<9)
 #define BOTTOM         (1u<<10)
+#define USER_GIVEN     (1u<<25) /* given directly by the user */
 #define TRACK_LINEAR   (1u<<26)
-#define ALL_REV_FLAGS  (((1u<<11)-1) | TRACK_LINEAR)
+#define ALL_REV_FLAGS  (((1u<<11)-1) | USER_GIVEN | TRACK_LINEAR)
 
 #define DECORATE_SHORT_REFS    1
 #define DECORATE_FULL_REFS     2
diff --git a/t/t5317-pack-objects-filter-objects.sh 
b/t/t5317-pack-objects-filter-objects.sh
index 1b0acc383b..6710c8bc8c 100755
--- a/t/t5317-pack-objects-filter-objects.sh
+++ b/t/t5317-pack-objects-filter-objects.sh
@@ -160,6 +160,22 @@ test_expect_success 'verify blob:limit=1k' '
        test_cmp observed expected
 '
 
+test_expect_success 'verify explicitly specifying oversized blob in input' '
+       git -C r2 ls-files -s large.1000 large.10000 \
+               | awk -f print_2.awk \
+               | sort >expected &&
+       git -C r2 pack-objects --rev --stdout --filter=blob:limit=1k 
>filter.pack <<-EOF &&
+       HEAD
+       $(git -C r2 rev-parse HEAD:large.10000)
+       EOF
+       git -C r2 index-pack ../filter.pack &&
+       git -C r2 verify-pack -v ../filter.pack \
+               | grep blob \
+               | awk -f print_1.awk \
+               | sort >observed &&
+       test_cmp observed expected
+'
+
 test_expect_success 'verify blob:limit=1m' '
        git -C r2 ls-files -s large.1000 large.10000 \
                | awk -f print_2.awk \
diff --git a/t/t5616-partial-clone.sh b/t/t5616-partial-clone.sh
index cee5565367..8a2bf86491 100755
--- a/t/t5616-partial-clone.sh
+++ b/t/t5616-partial-clone.sh
@@ -154,4 +154,20 @@ test_expect_success 'partial clone with 
transfer.fsckobjects=1 uses index-pack -
        grep "git index-pack.*--fsck-objects" trace
 '
 
+test_expect_success 'partial clone fetches blobs pointed to by refs even if 
normally filtered out' '
+       rm -rf src dst &&
+       git init src &&
+       test_commit -C src x &&
+       test_config -C src uploadpack.allowfilter 1 &&
+       test_config -C src uploadpack.allowanysha1inwant 1 &&
+
+       # Create a tag pointing to a blob.
+       BLOB=$(echo blob-contents | git -C src hash-object --stdin -w) &&
+       git -C src tag myblob "$BLOB" &&
+
+       git clone --filter="blob:none" "file://$(pwd)/src" dst 2>err &&
+       ! grep "does not point to a valid object" err &&
+       git -C dst fsck
+'
+
 test_done
-- 
2.18.0.203.gfac676dfb9-goog

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