fix:after compliance applied,the relationship concerning the original one should be omitted (#4419)

---------
Signed-off-by: Yuntao Hu <victorhu493@gmail.com>

internal/relationship/index.go

@@ -79,6 +79,10 @@ func (i *Index) Remove(id artifact.ID) {
 
 func (i *Index) Replace(ogID artifact.ID, replacement artifact.Identifiable) {
 	for _, mapped := range fromMappedByID(i.fromID, ogID) {
+		// the stale relationship(i.e. if there's an elder ID in either side) should be discarded
+		if len(fromMappedByID(i.toID, mapped.relationship.To.ID())) == 0 {
+			continue
+		}
 		i.Add(artifact.Relationship{
 			From: replacement,
 			To:   mapped.relationship.To,
@@ -87,6 +91,10 @@ func (i *Index) Replace(ogID artifact.ID, replacement artifact.Identifiable) {
 	}
 
 	for _, mapped := range fromMappedByID(i.toID, ogID) {
+		// same as the above
+		if len(fromMappedByID(i.fromID, mapped.relationship.To.ID())) == 0 {
+			continue
+		}
 		i.Add(artifact.Relationship{
 			From: mapped.relationship.From,
 			To:   replacement,

syft/pkg/cataloger/golang/parse_go_binary.go

@@ -98,6 +98,24 @@ func createModuleRelationships(main pkg.Package, deps []pkg.Package) []artifact.
 	return relationships
 }
 
+// moduleEqual is used to deduplicate go modules especially the sub module may be identical to the main one
+func moduleEqual(lhs, rhs *debug.Module) bool {
+	if lhs == rhs {
+		return true
+	}
+	if lhs == nil || rhs == nil {
+		return false
+	}
+
+	if lhs.Path != rhs.Path ||
+		lhs.Version != rhs.Version ||
+		lhs.Sum != rhs.Sum {
+		return false
+	}
+
+	return moduleEqual(lhs.Replace, rhs.Replace)
+}
+
 var emptyModule debug.Module
 var moduleFromPartialPackageBuild = debug.Module{Path: "command-line-arguments"}
 
@@ -115,7 +133,9 @@ func (c *goBinaryCataloger) buildGoPkgInfo(ctx context.Context, resolver file.Re
 		if dep == nil {
 			continue
 		}
-
+		if moduleEqual(dep, &mod.Main) {
+			continue
+		}
 		lics := c.licenseResolver.getLicenses(ctx, resolver, dep.Path, dep.Version)
 		gover, experiments := getExperimentsFromVersion(mod.GoVersion)
 

syft/pkg/cataloger/golang/parse_go_binary_test.go

@@ -847,6 +847,86 @@ func TestBuildGoPkgInfo(t *testing.T) {
 				unmodifiedMain,
 			},
 		},
+		{
+			name: "parse a populated mod string and returns packages when a replace directive and synthetic main module 'command line arguments' exists",
+			mod: &extendedBuildInfo{
+				BuildInfo: &debug.BuildInfo{
+					GoVersion: goCompiledVersion,
+					Main:      debug.Module{Path: "command-line-arguments", Version: devel},
+					Settings: []debug.BuildSetting{
+						{Key: "GOARCH", Value: archDetails},
+						{Key: "GOOS", Value: "linux"},
+						{Key: "GOAMD64", Value: "v1"},
+					},
+					Path: "command-line-arguments",
+					Deps: []*debug.Module{
+						{
+							Path:    "example.com/mylib",
+							Version: "v0.0.0",
+							Replace: &debug.Module{
+								Path:    "./mylib",
+								Version: devel,
+							},
+						},
+						{
+							Path:    "command-line-arguments",
+							Version: devel,
+						},
+					},
+				},
+				cryptoSettings: nil,
+				arch:           archDetails,
+			},
+			expected: []pkg.Package{
+				{
+					Name:     "example.com/mylib",
+					Version:  "",
+					PURL:     "pkg:golang/example.com/mylib",
+					Language: pkg.Go,
+					Type:     pkg.GoModulePkg,
+					Locations: file.NewLocationSet(
+						file.NewLocationFromCoordinates(
+							file.Coordinates{
+								RealPath:     "/a-path",
+								FileSystemID: "layer-id",
+							},
+						).WithAnnotation(pkg.EvidenceAnnotationKey, pkg.PrimaryEvidenceAnnotation),
+					),
+					Metadata: pkg.GolangBinaryBuildinfoEntry{
+						GoCompiledVersion: goCompiledVersion,
+						Architecture:      archDetails,
+						H1Digest:          "",
+						MainModule:        "command-line-arguments",
+					},
+				},
+				{
+					Name:     "command-line-arguments",
+					Version:  "",
+					PURL:     "pkg:golang/command-line-arguments",
+					Language: pkg.Go,
+					Type:     pkg.GoModulePkg,
+					Locations: file.NewLocationSet(
+						file.NewLocationFromCoordinates(
+							file.Coordinates{
+								RealPath:     "/a-path",
+								FileSystemID: "layer-id",
+							},
+						).WithAnnotation(pkg.EvidenceAnnotationKey, pkg.PrimaryEvidenceAnnotation),
+					),
+					Metadata: pkg.GolangBinaryBuildinfoEntry{
+						BuildSettings: pkg.KeyValues{
+							{Key: "GOARCH", Value: "amd64"},
+							{Key: "GOOS", Value: "linux"},
+							{Key: "GOAMD64", Value: "v1"},
+						},
+						GoCompiledVersion: goCompiledVersion,
+						Architecture:      archDetails,
+						H1Digest:          "",
+						MainModule:        "command-line-arguments",
+					},
+				},
+			},
+		},
 		{
 			name: "parse main mod and replace devel with pattern from binary contents",
 			cfg: func() *CatalogerConfig {