diff --git a/internal/engine/engine.go b/internal/engine/engine.go
index c8b5f37..a70e4df 100644
--- a/internal/engine/engine.go
+++ b/internal/engine/engine.go
@@ -54,7 +54,7 @@ var purposeMap = map[string]string{
 	"lib":        "Shared library code",
 	"utils":      "Utility functions",
 	"services":   "Business logic services",
-	"middleware":  "HTTP middleware",
+	"middleware": "HTTP middleware",
 	"cli":        "Command-line interface",
 	"schema":     "Data schema definitions",
 	"renderer":   "Output renderers",
@@ -108,6 +108,46 @@ func generateAddFeatureHint(modules map[string]schema.ModuleInfo, entrypoints []
 	return ""
 }
 
+func filterRetainedModules(names []string, retained map[string]bool) []string {
+	if len(names) == 0 {
+		return nil
+	}
+	out := make([]string, 0, len(names))
+	for _, name := range names {
+		if retained[name] {
+			out = append(out, name)
+		}
+	}
+	return out
+}
+
+func rankMostDepended(modules map[string]schema.ModuleInfo) []string {
+	names := make([]string, 0, len(modules))
+	for name := range modules {
+		names = append(names, name)
+	}
+	sort.SliceStable(names, func(i, j int) bool {
+		ci := len(modules[names[i]].DependedBy)
+		cj := len(modules[names[j]].DependedBy)
+		if ci != cj {
+			return ci > cj
+		}
+		return names[i] < names[j]
+	})
+	return names
+}
+
+func findIsolatedModules(modules map[string]schema.ModuleInfo) []string {
+	var isolated []string
+	for name, mod := range modules {
+		if len(mod.DependsOn) == 0 && len(mod.DependedBy) == 0 {
+			isolated = append(isolated, name)
+		}
+	}
+	sort.Strings(isolated)
+	return isolated
+}
+
 // detectDoNotTouch returns paths that should generally not be modified by hand.
 func detectDoNotTouch(root string) []string {
 	candidates := []string{"migrations", "vendor", "generated", "proto", ".github"}
@@ -439,6 +479,14 @@ func assembleIndex(
 		allMods = allMods[:maxModules]
 	}
 
+	retainedModules := make(map[string]bool, len(allMods))
+	for _, mod := range allMods {
+		if strings.HasPrefix(mod.Name, "testdata") {
+			continue
+		}
+		retainedModules[mod.Name] = true
+	}
+
 	modules := map[string]schema.ModuleInfo{}
 	for _, mod := range allMods {
 		if strings.HasPrefix(mod.Name, "testdata") {
@@ -491,8 +539,8 @@ func assembleIndex(
 			FileList:   fileList,
 			Exports:    exports,
 			TypeDefs:   typeDefs,
-			DependsOn:  mod.DependsOn,
-			DependedBy: mod.DependedBy,
+			DependsOn:  filterRetainedModules(mod.DependsOn, retainedModules),
+			DependedBy: filterRetainedModules(mod.DependedBy, retainedModules),
 			Activity:   activityLevel,
 		}
 	}
@@ -504,14 +552,17 @@ func assembleIndex(
 		if strings.HasPrefix(e.From, "testdata") || strings.HasPrefix(e.To, "testdata") {
 			continue
 		}
+		if !retainedModules[e.From] || !retainedModules[e.To] {
+			continue
+		}
 		schemaEdges = append(schemaEdges, [2]string{e.From, e.To})
 	}
-	mostDepended := g.MostDepended()
+	mostDepended := rankMostDepended(modules)
 	// Cap most-depended list.
 	if len(mostDepended) > 10 {
 		mostDepended = mostDepended[:10]
 	}
-	isolated := g.Isolated()
+	isolated := findIsolatedModules(modules)
 
 	// --- Git ---
 	hotFiles := make([]schema.HotFile, len(activity.HotFiles))
diff --git a/internal/engine/engine_test.go b/internal/engine/engine_test.go
new file mode 100644
index 0000000..e7c1fa2
--- /dev/null
+++ b/internal/engine/engine_test.go
@@ -0,0 +1,74 @@
+package engine
+
+import (
+	"testing"
+
+	"github.com/glincker/stacklit/internal/config"
+	"github.com/glincker/stacklit/internal/git"
+	"github.com/glincker/stacklit/internal/graph"
+	"github.com/glincker/stacklit/internal/monorepo"
+	"github.com/glincker/stacklit/internal/parser"
+)
+
+func TestAssembleIndexFiltersTrimmedModuleReferences(t *testing.T) {
+	files := []*parser.FileInfo{
+		{Path: "src/api/index.ts", Language: "TypeScript", Imports: []string{"src/auth", "src/db"}, LineCount: 50},
+		{Path: "src/auth/service.ts", Language: "TypeScript", Imports: []string{"src/db"}, LineCount: 40},
+		{Path: "src/db/pool.ts", Language: "TypeScript", Exports: []string{"Pool"}, LineCount: 30},
+	}
+
+	g := graph.Build(files, graph.BuildOptions{MaxDepth: 4})
+	cfg := config.DefaultConfig()
+	cfg.MaxModules = 2
+
+	idx := assembleIndex(
+		".",
+		&monorepo.Result{Type: "single"},
+		[]string{"src/api/index.ts", "src/auth/service.ts", "src/db/pool.ts"},
+		files,
+		g,
+		&git.Activity{},
+		map[string][]byte{},
+		cfg,
+	)
+
+	if len(idx.Modules) != 2 {
+		t.Fatalf("expected 2 retained modules, got %d: %v", len(idx.Modules), idx.Modules)
+	}
+	if _, ok := idx.Modules["src/db"]; ok {
+		t.Fatalf("expected trimmed module src/db to be omitted from modules, got %v", idx.Modules)
+	}
+
+	api := idx.Modules["src/api"]
+	if len(api.DependsOn) != 1 || api.DependsOn[0] != "src/auth" {
+		t.Fatalf("expected src/api depends_on to retain only src/auth, got %v", api.DependsOn)
+	}
+
+	auth := idx.Modules["src/auth"]
+	if len(auth.DependsOn) != 0 {
+		t.Fatalf("expected src/auth depends_on to drop trimmed src/db reference, got %v", auth.DependsOn)
+	}
+	if len(auth.DependedBy) != 1 || auth.DependedBy[0] != "src/api" {
+		t.Fatalf("expected src/auth depended_by to contain only src/api, got %v", auth.DependedBy)
+	}
+
+	if len(idx.Dependencies.Edges) != 1 || idx.Dependencies.Edges[0] != ([2]string{"src/api", "src/auth"}) {
+		t.Fatalf("expected only retained edge src/api -> src/auth, got %v", idx.Dependencies.Edges)
+	}
+
+	if len(idx.Dependencies.MostDepended) < 2 {
+		t.Fatalf("expected ranked retained modules, got %v", idx.Dependencies.MostDepended)
+	}
+	if idx.Dependencies.MostDepended[0] != "src/auth" {
+		t.Fatalf("expected src/auth to be most depended after trimming, got %v", idx.Dependencies.MostDepended)
+	}
+	for _, name := range idx.Dependencies.MostDepended {
+		if name == "src/db" {
+			t.Fatalf("expected trimmed module src/db to be absent from most_depended, got %v", idx.Dependencies.MostDepended)
+		}
+	}
+
+	if len(idx.Dependencies.Isolated) != 0 {
+		t.Fatalf("expected no isolated retained modules, got %v", idx.Dependencies.Isolated)
+	}
+}