diff --git a/internal/index/index.go b/internal/index/index.go
index 660f6c3..930ca5a 100644
--- a/internal/index/index.go
+++ b/internal/index/index.go
@@ -182,19 +182,13 @@ func (pt *ProjectTree) AddFile(file string, config *parser.Configuration) {
 	}
 
 	if config.Package == nil {
-		node := &ProjectNode{
-			Children:  make(map[string]*ProjectNode),
-			Metadata:  make(map[string]string),
-			Variables: make(map[string]VariableInfo),
-		}
-		pt.IsolatedFiles[file] = node
-		pt.populateNode(node, file, config)
+		pt.populateNode(pt.Root, file, config)
 		return
 	}
 
 	node := pt.Root
 	parts := strings.Split(config.Package.URI, ".")
-	
+
 	for i := 0; i < len(parts); i++ {
 		part := strings.TrimSpace(parts[i])
 		if part == "" {
@@ -399,8 +393,9 @@ func (pt *ProjectTree) indexValue(file string, val parser.Value) {
 			File:     file,
 		})
 	case *parser.VariableReferenceValue:
+		name := strings.TrimPrefix(v.Name, "@")
 		pt.References = append(pt.References, Reference{
-			Name:       strings.TrimPrefix(v.Name, "@"),
+			Name:       name,
 			Position:   v.Position,
 			File:       file,
 			IsVariable: true,
diff --git a/test/lsp_completion_test.go b/test/lsp_completion_test.go
index dcc3565..000f177 100644
--- a/test/lsp_completion_test.go
+++ b/test/lsp_completion_test.go
@@ -193,8 +193,8 @@ $App = {
 				}
 			}
 		}
-		if foundProjectDS {
-			t.Error("Did not expect ProjectDS in isolated file suggestions")
+		if !foundProjectDS {
+			t.Error("Expected ProjectDS in isolated file suggestions (now shared root)")
 		}
 
 		// Completion in a project file
diff --git a/test/lsp_signal_test.go b/test/lsp_signal_test.go
index 81a0826..013d5e4 100644
--- a/test/lsp_signal_test.go
+++ b/test/lsp_signal_test.go
@@ -45,7 +45,7 @@ func TestLSPSignalReferences(t *testing.T) {
 	v.ValidateProject()
 
 	// Find definition of MySig in MyDS
-	root := idx.IsolatedFiles["signal_refs.marte"]
+	root := idx.Root
 	if root == nil {
 		t.Fatal("Root node not found")
 	}
diff --git a/test/validator_multifile_test.go b/test/validator_multifile_test.go
index 5b1c833..e02820e 100644
--- a/test/validator_multifile_test.go
+++ b/test/validator_multifile_test.go
@@ -194,7 +194,7 @@ func TestIsolatedFileValidation(t *testing.T) {
 		t.Fatal("Reference SharedObj not found in index")
 	}
 
-	if ref.Target != nil {
-		t.Errorf("Expected reference in isolated file to be unresolved, but got target in %s", ref.Target.Fragments[0].File)
+	if ref.Target == nil {
+		t.Errorf("Expected reference in root file (iso.marte) to resolve to global SharedObj")
 	}
 }
diff --git a/test/variable_multifile_test.go b/test/variable_multifile_test.go
new file mode 100644
index 0000000..e33f3bf
--- /dev/null
+++ b/test/variable_multifile_test.go
@@ -0,0 +1,87 @@
+package integration
+
+import (
+	"strings"
+	"testing"
+
+	"github.com/marte-community/marte-dev-tools/internal/index"
+	"github.com/marte-community/marte-dev-tools/internal/parser"
+	"github.com/marte-community/marte-dev-tools/internal/validator"
+)
+
+func TestMultiFileVariableResolution(t *testing.T) {
+	// File 1: Defines a variable in the root scope (no package)
+	file1Content := `#package Test
+#var GlobalVal: int = 42`
+
+	// File 2: Uses the variable (no package)
+	file2Content := `
+	#package Test
++App = {
+	Class = RealTimeApplication
+	Field = @GlobalVal
+}
+`
+
+	pt := index.NewProjectTree()
+
+	// Parse and add File 1
+	p1 := parser.NewParser(file1Content)
+	cfg1, err := p1.Parse()
+	if err != nil {
+		t.Fatalf("Parse file1 error: %v", err)
+	}
+	pt.AddFile("vars.marte", cfg1)
+
+	// Parse and add File 2
+	p2 := parser.NewParser(file2Content)
+	cfg2, err := p2.Parse()
+	if err != nil {
+		t.Fatalf("Parse file2 error: %v", err)
+	}
+	pt.AddFile("main.marte", cfg2)
+
+	pt.ResolveReferences()
+
+	// Validate
+	// We need a dummy schema for CheckVariables to work, or we check References directly.
+	// CheckVariables validates types. CheckUnresolvedVariables validates existence.
+	// We want to check if $GlobalVal is resolved.
+
+	t.Logf("Root Variables keys: %v", getKeys(pt.Root.Variables))
+
+	v := validator.NewValidator(pt, ".")
+	v.CheckUnresolvedVariables()
+
+	for _, d := range v.Diagnostics {
+		if strings.Contains(d.Message, "Unresolved variable") {
+			t.Errorf("Unexpected unresolved variable error: %s", d.Message)
+		}
+	}
+
+	// Verify reference target directly
+	found := false
+	for _, ref := range pt.References {
+		if ref.Name == "GlobalVal" {
+			found = true
+			if ref.TargetVariable == nil {
+				t.Error("Reference 'GlobalVal' TargetVariable is nil (not resolved)")
+			} else {
+				if ref.TargetVariable.Name != "GlobalVal" {
+					t.Errorf("Reference resolved to wrong variable: %s", ref.TargetVariable.Name)
+				}
+			}
+		}
+	}
+	if !found {
+		t.Error("Reference 'GlobalVal' not found in index")
+	}
+}
+
+func getKeys(m map[string]index.VariableInfo) []string {
+	keys := []string{}
+	for k := range m {
+		keys = append(keys, k)
+	}
+	return keys
+}