feat: handle orphan indirect depenencies

Signed-off-by: knqyf263 <[email protected]>

pkg/fanal/analyzer/language/golang/mod/mod.go

@@ -101,6 +101,9 @@ func (a *gomodAnalyzer) PostAnalyze(_ context.Context, input analyzer.PostAnalys
 		a.logger.Warn("Unable to collect additional info", log.Err(err))
 	}
 
+	// Add orphan indirect dependencies under the main module
+	a.addOrphanIndirectDepsUnderRoot(apps)
+
 	return &analyzer.AnalysisResult{
 		Applications: apps,
 	}, nil
@@ -212,6 +215,40 @@ func (a *gomodAnalyzer) collectDeps(modDir, pkgID string) (types.Dependency, err
 	}, nil
 }
 
+// addOrphanIndirectDepsUnderRoot handles indirect dependencies that have no identifiable parent packages in the dependency tree.
+// This situation can occur when:
+// - $GOPATH/pkg directory doesn't exist
+// - Module cache is incomplete
+// - etc.
+//
+// In such cases, indirect packages become "orphaned" - they exist in the dependency list
+// but have no connection to the dependency tree. This function resolves this issue by:
+// 1. Finding the root (main) module
+// 2. Identifying all indirect dependencies that have no parent packages
+// 3. Adding these orphaned indirect dependencies under the main module
+//
+// This ensures that all packages remain visible in the dependency tree, even when the complete
+// dependency chain cannot be determined.
+func (a *gomodAnalyzer) addOrphanIndirectDepsUnderRoot(apps []types.Application) {
+	for _, app := range apps {
+		// Find the main module
+		_, rootIdx, found := lo.FindIndexOf(app.Packages, func(pkg types.Package) bool {
+			return pkg.Relationship == types.RelationshipRoot
+		})
+		if !found {
+			continue
+		}
+
+		// Collect all orphan indirect dependencies that are unable to identify parents
+		parents := app.Packages.ParentDeps()
+		orphanDeps := lo.FilterMap(app.Packages, func(pkg types.Package, _ int) (string, bool) {
+			return pkg.ID, pkg.Relationship == types.RelationshipIndirect && len(parents[pkg.ID]) == 0
+		})
+		// Add orphan indirect dependencies under the main module
+		app.Packages[rootIdx].DependsOn = append(app.Packages[rootIdx].DependsOn, orphanDeps...)
+	}
+}
+
 func parse(fsys fs.FS, path string, parser language.Parser) (*types.Application, error) {
 	f, err := fsys.Open(path)
 	if err != nil {

pkg/fanal/analyzer/language/golang/mod/mod_test.go

@@ -116,6 +116,69 @@ func Test_gomodAnalyzer_Analyze(t *testing.T) {
 				},
 			},
 		},
+		{
+			name: "no pkg dir found",
+			files: []string{
+				"testdata/no-pkg-found/mod",
+			},
+			want: &analyzer.AnalysisResult{
+				Applications: []types.Application{
+					{
+						Type:     types.GoModule,
+						FilePath: "go.mod",
+						Packages: types.Packages{
+							{
+								ID:           "github.com/org/repo",
+								Name:         "github.com/org/repo",
+								Relationship: types.RelationshipRoot,
+								DependsOn: []string{
+									"github.com/aquasecurity/[email protected]",
+									"github.com/aquasecurity/[email protected]",
+									"golang.org/x/[email protected]", // No parent found, so it's added here.
+								},
+								ExternalReferences: []types.ExternalRef{
+									{
+										Type: types.RefVCS,
+										URL:  "https://github.com/org/repo",
+									},
+								},
+							},
+							{
+								ID:           "github.com/aquasecurity/[email protected]",
+								Name:         "github.com/aquasecurity/go-dep-parser",
+								Version:      "v1.0.0",
+								Relationship: types.RelationshipDirect,
+								ExternalReferences: []types.ExternalRef{
+									{
+										Type: types.RefVCS,
+										URL:  "https://github.com/aquasecurity/go-dep-parser",
+									},
+								},
+							},
+							{
+								ID:           "github.com/aquasecurity/[email protected]",
+								Name:         "github.com/aquasecurity/go-version",
+								Version:      "v1.0.1",
+								Relationship: types.RelationshipDirect,
+								ExternalReferences: []types.ExternalRef{
+									{
+										Type: types.RefVCS,
+										URL:  "https://github.com/aquasecurity/go-version",
+									},
+								},
+							},
+							{
+								ID:           "golang.org/x/[email protected]",
+								Name:         "golang.org/x/xerrors",
+								Version:      "v0.0.0-20200804184101-5ec99f83aff1",
+								Relationship: types.RelationshipIndirect,
+								Indirect:     true,
+							},
+						},
+					},
+				},
+			},
+		},
 		{
 			name: "less than 1.17",
 			files: []string{