upload-pack: send refs' objects despite "filter"

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 <jonathantanmy@google.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
diff --git a/t/t5317-pack-objects-filter-objects.sh b/t/t5317-pack-objects-filter-objects.sh
index 1b0acc3..6710c8b 100755
--- a/t/t5317-pack-objects-filter-objects.sh
+++ b/t/t5317-pack-objects-filter-objects.sh
@@ -160,6 +160,22 @@
 	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 \