fix: de-duplicate same dpkg packages with different filePaths from different layers

pkg/fanal/applier/docker.go

@@ -1,6 +1,7 @@
 package applier
 
 import (
+	"cmp"
 	"fmt"
 	"strings"
 	"time"
@@ -13,7 +14,9 @@ import (
 	ftypes "github.com/aquasecurity/trivy/pkg/fanal/types"
 	"github.com/aquasecurity/trivy/pkg/log"
 	"github.com/aquasecurity/trivy/pkg/purl"
+	"github.com/aquasecurity/trivy/pkg/scanner/utils"
 	"github.com/aquasecurity/trivy/pkg/types"
+	xslices "github.com/aquasecurity/trivy/pkg/x/slices"
 )
 
 type Config struct {
@@ -232,6 +235,12 @@ func ApplyLayers(layers []ftypes.BlobInfo) ftypes.ArtifactDetail {
 		}
 	}
 
+	// De-duplicate same debian packages from different dirs
+	// cf. https://github.com/aquasecurity/trivy/issues/8297
+	mergedLayer.Packages = xslices.ZeroToNil(lo.UniqBy(mergedLayer.Packages, func(pkg ftypes.Package) string {
+		return cmp.Or(pkg.ID, fmt.Sprintf("%s@%s", pkg.Name, utils.FormatVersion(pkg)))
+	}))
+
 	for _, app := range mergedLayer.Applications {
 		for i, pkg := range app.Packages {
 			// Skip lookup for SBOM

pkg/fanal/applier/docker_test.go

@@ -254,6 +254,61 @@ func TestApplyLayers(t *testing.T) {
 				},
 			},
 		},
+		{
+			name: "happy path with duplicate of debian packages",
+			inputLayers: []types.BlobInfo{
+				{
+					SchemaVersion: 2,
+					DiffID:        "sha256:96e320b34b5478d8b369ca43ffaa88ff6dd9499ec72b792ca21b1e8b0c55670f",
+					PackageInfos: []types.PackageInfo{
+						{
+							FilePath: "var/lib/dpkg/status.d/libssl1",
+							Packages: types.Packages{
+								{
+									ID:      "[email protected]+deb11u3",
+									Name:    "libssl1.1",
+									Version: "1.1.1n",
+									Release: "0+deb11u3",
+								},
+							},
+						},
+					},
+				},
+				{
+					SchemaVersion: 2,
+					DiffID:        "sha256:5e087d956f3e62bd034dd0712bc4cbef8fda55fba0b11a7d0564f294887c7079",
+					PackageInfos: []types.PackageInfo{
+						{
+							FilePath: "var/lib/dpkg/status.d/libssl1.1",
+							Packages: types.Packages{
+								{
+									ID:      "[email protected]+deb11u3",
+									Name:    "libssl1.1",
+									Version: "1.1.1n",
+									Release: "0+deb11u3",
+								},
+							},
+						},
+					},
+				},
+			},
+			want: types.ArtifactDetail{
+				Packages: types.Packages{
+					{
+						ID:      "[email protected]+deb11u3",
+						Name:    "libssl1.1",
+						Version: "1.1.1n",
+						Release: "0+deb11u3",
+						Identifier: types.PkgIdentifier{
+							UID: "522a5c3b263d1357",
+						},
+						Layer: types.Layer{
+							DiffID: "sha256:96e320b34b5478d8b369ca43ffaa88ff6dd9499ec72b792ca21b1e8b0c55670f",
+						},
+					},
+				},
+			},
+		},
 		{
 			name: "happy path with digests in libs/packages (as for SBOM)",
 			inputLayers: []types.BlobInfo{

pkg/x/slices/slices.go

@@ -1,5 +1,6 @@
 package slices
 
+// ZeroToNil returns nil, if slice is empty
 func ZeroToNil[T any](t []T) []T {
 	if len(t) == 0 {
 		return nil