diff --git a/internal/project/project.go b/internal/project/project.go
index 7a3124f..e68c34d 100644
--- a/internal/project/project.go
+++ b/internal/project/project.go
@@ -138,11 +138,15 @@ func (p *Project) ValidateLayout() error {
 		}
 	}
 
-	for label, path := range map[string]string{
-		"paths.source": p.SourceDir(),
-		"paths.assets": p.AssetsDir(),
-		"paths.build":  p.BuildDir(),
+	for label, pathFn := range map[string]func() string{
+		"paths.source": p.SourceDir,
+		"paths.assets": p.AssetsDir,
+		"paths.build":  p.BuildDir,
 	} {
+		path := pathFn()
+		if path == "" || filepath.Clean(path) == p.Root {
+			continue
+		}
 		info, err := os.Stat(path)
 		if err != nil {
 			if label == "paths.assets" && errors.Is(err, os.ErrNotExist) {
@@ -164,12 +168,21 @@ func (p *Project) ValidateLayout() error {
 }
 
 func (p *Project) Scan() error {
-	sourceFiles, sourceExts, err := scanDir(p.SourceDir(), func(path string) bool {
-		ext := strings.ToLower(filepath.Ext(path))
-		return ext == ".json" || ext == ".nss"
-	})
-	if err != nil {
-		return fmt.Errorf("scan source tree: %w", err)
+	var sourceFiles []string
+	var sourceExts []string
+
+	sourceDir := p.SourceDir()
+	if sourceDir != "" && filepath.Clean(sourceDir) != p.Root {
+		var err error
+		sourceFiles, sourceExts, err = scanDir(sourceDir, func(path string) bool {
+			ext := strings.ToLower(filepath.Ext(path))
+			return ext == ".json" || ext == ".nss"
+		})
+		if err != nil {
+			if !errors.Is(err, os.ErrNotExist) {
+				return fmt.Errorf("scan source tree: %w", err)
+			}
+		}
 	}
 
 	assetFiles, _, err := scanDir(p.AssetsDir(), func(path string) bool {