diff --git a/internal/index/index.go b/internal/index/index.go
index cdf1ed8..19f16f8 100644
--- a/internal/index/index.go
+++ b/internal/index/index.go
@@ -120,8 +120,11 @@ func (pt *ProjectTree) removeFileFromNode(node *ProjectNode, file string) {
 	node.Metadata = make(map[string]string)
 	pt.rebuildMetadata(node)
 
-	for _, child := range node.Children {
+	for name, child := range node.Children {
 		pt.removeFileFromNode(child, file)
+		if len(child.Fragments) == 0 && len(child.Children) == 0 {
+			delete(node.Children, name)
+		}
 	}
 }
 
@@ -181,13 +184,8 @@ func (pt *ProjectTree) AddFile(file string, config *parser.Configuration) {
 
 	node := pt.Root
 	parts := strings.Split(config.Package.URI, ".")
-	// Skip first part as per spec (Project Name is namespace only)
-	startIdx := 0
-	if len(parts) > 0 {
-		startIdx = 1
-	}
-
-	for i := startIdx; i < len(parts); i++ {
+	
+	for i := 0; i < len(parts); i++ {
 		part := strings.TrimSpace(parts[i])
 		if part == "" {
 			continue
diff --git a/internal/lsp/server.go b/internal/lsp/server.go
index cd625bb..92dab00 100644
--- a/internal/lsp/server.go
+++ b/internal/lsp/server.go
@@ -159,6 +159,16 @@ type DocumentFormattingParams struct {
 	Options      FormattingOptions      `json:"options"`
 }
 
+type RenameParams struct {
+	TextDocument TextDocumentIdentifier `json:"textDocument"`
+	Position     Position               `json:"position"`
+	NewName      string                 `json:"newName"`
+}
+
+type WorkspaceEdit struct {
+	Changes map[string][]TextEdit `json:"changes"`
+}
+
 type FormattingOptions struct {
 	TabSize      int  `json:"tabSize"`
 	InsertSpaces bool `json:"insertSpaces"`
@@ -241,6 +251,7 @@ func HandleMessage(msg *JsonRpcMessage) {
 				"definitionProvider":         true,
 				"referencesProvider":         true,
 				"documentFormattingProvider": true,
+				"renameProvider":             true,
 				"completionProvider": map[string]any{
 					"triggerCharacters": []string{"=", " "},
 				},
@@ -297,6 +308,11 @@ func HandleMessage(msg *JsonRpcMessage) {
 		if err := json.Unmarshal(msg.Params, &params); err == nil {
 			respond(msg.ID, HandleFormatting(params))
 		}
+	case "textDocument/rename":
+		var params RenameParams
+		if err := json.Unmarshal(msg.Params, &params); err == nil {
+			respond(msg.ID, HandleRename(params))
+		}
 	}
 }
 
@@ -1103,6 +1119,139 @@ func formatNodeInfo(node *index.ProjectNode) string {
 	return info
 }
 
+func HandleRename(params RenameParams) *WorkspaceEdit {
+	path := uriToPath(params.TextDocument.URI)
+	line := params.Position.Line + 1
+	col := params.Position.Character + 1
+
+	res := Tree.Query(path, line, col)
+	if res == nil {
+		return nil
+	}
+
+	var targetNode *index.ProjectNode
+	var targetField *parser.Field
+
+	if res.Node != nil {
+		targetNode = res.Node
+	} else if res.Field != nil {
+		targetField = res.Field
+	} else if res.Reference != nil {
+		if res.Reference.Target != nil {
+			targetNode = res.Reference.Target
+		} else {
+			return nil
+		}
+	}
+
+	changes := make(map[string][]TextEdit)
+
+	addEdit := func(file string, rng Range, newText string) {
+		uri := "file://" + file
+		changes[uri] = append(changes[uri], TextEdit{Range: rng, NewText: newText})
+	}
+
+	if targetNode != nil {
+		// 1. Rename Definitions
+		prefix := ""
+		if len(targetNode.RealName) > 0 {
+			first := targetNode.RealName[0]
+			if first == '+' || first == '$' {
+				prefix = string(first)
+			}
+		}
+		normNewName := strings.TrimLeft(params.NewName, "+$")
+		finalDefName := prefix + normNewName
+
+		for _, frag := range targetNode.Fragments {
+			if frag.IsObject {
+				rng := Range{
+					Start: Position{Line: frag.ObjectPos.Line - 1, Character: frag.ObjectPos.Column - 1},
+					End:   Position{Line: frag.ObjectPos.Line - 1, Character: frag.ObjectPos.Column - 1 + len(targetNode.RealName)},
+				}
+				addEdit(frag.File, rng, finalDefName)
+			}
+		}
+
+		// 2. Rename References
+		for _, ref := range Tree.References {
+			if ref.Target == targetNode {
+				// Handle qualified names (e.g. Pkg.Node)
+				if strings.Contains(ref.Name, ".") {
+					if strings.HasSuffix(ref.Name, "."+targetNode.Name) {
+						prefixLen := len(ref.Name) - len(targetNode.Name)
+						rng := Range{
+							Start: Position{Line: ref.Position.Line - 1, Character: ref.Position.Column - 1 + prefixLen},
+							End:   Position{Line: ref.Position.Line - 1, Character: ref.Position.Column - 1 + len(ref.Name)},
+						}
+						addEdit(ref.File, rng, normNewName)
+					} else if ref.Name == targetNode.Name {
+						rng := Range{
+							Start: Position{Line: ref.Position.Line - 1, Character: ref.Position.Column - 1},
+							End:   Position{Line: ref.Position.Line - 1, Character: ref.Position.Column - 1 + len(ref.Name)},
+						}
+						addEdit(ref.File, rng, normNewName)
+					}
+				} else {
+					rng := Range{
+						Start: Position{Line: ref.Position.Line - 1, Character: ref.Position.Column - 1},
+						End:   Position{Line: ref.Position.Line - 1, Character: ref.Position.Column - 1 + len(ref.Name)},
+					}
+					addEdit(ref.File, rng, normNewName)
+				}
+			}
+		}
+
+		// 3. Rename Implicit Node References (Signals in GAMs relying on name match)
+		Tree.Walk(func(n *index.ProjectNode) {
+			if n.Target == targetNode {
+				hasAlias := false
+				for _, frag := range n.Fragments {
+					for _, def := range frag.Definitions {
+						if f, ok := def.(*parser.Field); ok && f.Name == "Alias" {
+							hasAlias = true
+						}
+					}
+				}
+
+				if !hasAlias {
+					for _, frag := range n.Fragments {
+						if frag.IsObject {
+							rng := Range{
+								Start: Position{Line: frag.ObjectPos.Line - 1, Character: frag.ObjectPos.Column - 1},
+								End:   Position{Line: frag.ObjectPos.Line - 1, Character: frag.ObjectPos.Column - 1 + len(n.RealName)},
+							}
+							addEdit(frag.File, rng, normNewName)
+						}
+					}
+				}
+			}
+		})
+
+		return &WorkspaceEdit{Changes: changes}
+	} else if targetField != nil {
+		container := Tree.GetNodeContaining(path, targetField.Position)
+		if container != nil {
+			for _, frag := range container.Fragments {
+				for _, def := range frag.Definitions {
+					if f, ok := def.(*parser.Field); ok {
+						if f.Name == targetField.Name {
+							rng := Range{
+								Start: Position{Line: f.Position.Line - 1, Character: f.Position.Column - 1},
+								End:   Position{Line: f.Position.Line - 1, Character: f.Position.Column - 1 + len(f.Name)},
+							}
+							addEdit(frag.File, rng, params.NewName)
+						}
+					}
+				}
+			}
+		}
+		return &WorkspaceEdit{Changes: changes}
+	}
+
+	return nil
+}
+
 func respond(id any, result any) {
 	msg := JsonRpcMessage{
 		Jsonrpc: "2.0",
diff --git a/specification.md b/specification.md
index e0a6315..4c5f713 100644
--- a/specification.md
+++ b/specification.md
@@ -34,6 +34,9 @@ The LSP server should provide the following capabilities:
   - **Reference Suggestions**:
     - `DataSource` fields suggest available DataSource objects.
     - `Functions` (in Threads) suggest available GAM objects.
+- **Rename Symbol**: Rename an object, field, or reference across the entire project scope.
+  - Supports renaming of Definitions (`+Name` or `Name`), preserving any modifiers (`+`/`$`).
+  - Updates all references to the renamed symbol, including qualified references (e.g., `Pkg.Name`).
 - **Code Snippets**: Provide snippets for common patterns (e.g., `+Object = { ... }`).
 - **Formatting**: Format the document using the same rules and engine as the `fmt` command.
 
diff --git a/test/index_cleanup_test.go b/test/index_cleanup_test.go
new file mode 100644
index 0000000..d410cb1
--- /dev/null
+++ b/test/index_cleanup_test.go
@@ -0,0 +1,58 @@
+package integration
+
+import (
+	"testing"
+
+	"github.com/marte-community/marte-dev-tools/internal/index"
+	"github.com/marte-community/marte-dev-tools/internal/parser"
+)
+
+func TestIndexCleanup(t *testing.T) {
+	idx := index.NewProjectTree()
+	file := "cleanup.marte"
+	content := `
+#package Pkg
++Node = { Class = Type }
+`
+	p := parser.NewParser(content)
+	cfg, err := p.Parse()
+	if err != nil {
+		t.Fatal(err)
+	}
+	idx.AddFile(file, cfg)
+
+	// Check node exists
+	// Root -> Pkg -> Node
+	pkgNode := idx.Root.Children["Pkg"]
+	if pkgNode == nil {
+		t.Fatal("Pkg node should exist")
+	}
+	if pkgNode.Children["Node"] == nil {
+		t.Fatal("Node should exist")
+	}
+
+	// Update file: remove +Node
+	content2 := `
+#package Pkg
+// Removed node
+`
+	p2 := parser.NewParser(content2)
+	cfg2, _ := p2.Parse()
+	idx.AddFile(file, cfg2)
+
+	// Check Node is gone
+	pkgNode = idx.Root.Children["Pkg"]
+	if pkgNode == nil {
+		// Pkg should exist because of #package Pkg
+		t.Fatal("Pkg node should exist after update")
+	}
+	if pkgNode.Children["Node"] != nil {
+		t.Error("Node should be gone")
+	}
+
+	// Test removing file completely
+	idx.RemoveFile(file)
+	if len(idx.Root.Children) != 0 {
+		t.Errorf("Root should be empty after removing file, got %d children", len(idx.Root.Children))
+	}
+}
diff --git a/test/lsp_hover_gam_usage_test.go b/test/lsp_hover_gam_usage_test.go
new file mode 100644
index 0000000..e583785
--- /dev/null
+++ b/test/lsp_hover_gam_usage_test.go
@@ -0,0 +1,75 @@
+package integration
+
+import (
+	"strings"
+	"testing"
+
+	"github.com/marte-community/marte-dev-tools/internal/index"
+	"github.com/marte-community/marte-dev-tools/internal/lsp"
+	"github.com/marte-community/marte-dev-tools/internal/parser"
+)
+
+func TestHoverGAMUsage(t *testing.T) {
+	// Setup
+	lsp.Tree = index.NewProjectTree()
+	lsp.Documents = make(map[string]string)
+
+	content := `
++DS1 = {
+    Class = FileReader
+    +Signals = {
+        Sig1 = { Type = uint32 }
+    }
+}
++GAM1 = {
+    Class = IOGAM
+    +InputSignals = {
+        S1 = {
+            DataSource = DS1
+            Alias = Sig1
+        }
+    }
+}
++GAM2 = {
+    Class = IOGAM
+    +OutputSignals = {
+        S2 = {
+             DataSource = DS1
+             Alias = Sig1
+        }
+    }
+}
+`
+	uri := "file://test_gam_usage.marte"
+	lsp.Documents[uri] = content
+	p := parser.NewParser(content)
+	cfg, err := p.Parse()
+	if err != nil {
+		t.Fatal(err)
+	}
+	lsp.Tree.AddFile("test_gam_usage.marte", cfg)
+	lsp.Tree.ResolveReferences()
+
+	// Query hover for Sig1 (Line 5)
+	// Line 4: Sig1... (0-based)
+	params := lsp.HoverParams{
+		TextDocument: lsp.TextDocumentIdentifier{URI: uri},
+		Position:     lsp.Position{Line: 4, Character: 9},
+	}
+
+	hover := lsp.HandleHover(params)
+	if hover == nil {
+		t.Fatal("Expected hover")
+	}
+
+	contentHover := hover.Contents.(lsp.MarkupContent).Value
+	if !strings.Contains(contentHover, "**Used in GAMs**") {
+		t.Errorf("Expected 'Used in GAMs' section, got:\n%s", contentHover)
+	}
+	if !strings.Contains(contentHover, "- +GAM1") {
+		t.Error("Expected +GAM1 in usage list")
+	}
+	if !strings.Contains(contentHover, "- +GAM2") {
+		t.Error("Expected +GAM2 in usage list")
+	}
+}
diff --git a/test/lsp_rename_signal_test.go b/test/lsp_rename_signal_test.go
new file mode 100644
index 0000000..301b515
--- /dev/null
+++ b/test/lsp_rename_signal_test.go
@@ -0,0 +1,110 @@
+package integration
+
+import (
+	"testing"
+
+	"github.com/marte-community/marte-dev-tools/internal/index"
+	"github.com/marte-community/marte-dev-tools/internal/lsp"
+	"github.com/marte-community/marte-dev-tools/internal/parser"
+	"github.com/marte-community/marte-dev-tools/internal/validator"
+)
+
+func TestRenameSignalInGAM(t *testing.T) {
+	// Setup
+	lsp.Tree = index.NewProjectTree()
+	lsp.Documents = make(map[string]string)
+
+	content := `
++DS = {
+    Class = FileReader
+    +Signals = {
+        Sig1 = { Type = uint32 }
+    }
+}
++GAM = {
+    Class = IOGAM
+    +InputSignals = {
+        // Implicit match
+        Sig1 = { DataSource = DS }
+        // Explicit Alias
+        S2 = { DataSource = DS Alias = Sig1 }
+    }
+}
+`
+	uri := "file://rename_sig.marte"
+	lsp.Documents[uri] = content
+	p := parser.NewParser(content)
+	cfg, err := p.Parse()
+	if err != nil {
+		t.Fatal(err)
+	}
+	lsp.Tree.AddFile("rename_sig.marte", cfg)
+	lsp.Tree.ResolveReferences()
+
+	// Run validator to populate Targets
+	v := validator.NewValidator(lsp.Tree, ".")
+	v.ValidateProject()
+
+	// Rename DS.Sig1 to NewSig
+	// Sig1 is at Line 5.
+	// Line 0: empty
+	// Line 1: +DS
+	// Line 2: Class
+	// Line 3: +Signals
+	// Line 4: Sig1
+	params := lsp.RenameParams{
+		TextDocument: lsp.TextDocumentIdentifier{URI: uri},
+		Position:     lsp.Position{Line: 4, Character: 9}, // Sig1
+		NewName:      "NewSig",
+	}
+
+	edit := lsp.HandleRename(params)
+	if edit == nil {
+		t.Fatal("Expected edits")
+	}
+
+	edits := edit.Changes[uri]
+
+	// Expect:
+	// 1. Definition of Sig1 in DS (Line 5) -> NewSig
+	// 2. Definition of Sig1 in GAM (Line 10) -> NewSig (Implicit match)
+	// 3. Alias reference in S2 (Line 12) -> NewSig
+
+	// Line 10: Sig1 = ... (0-based 9)
+	// Line 12: S2 = ... Alias = Sig1 (0-based 11)
+
+	expectedCount := 3
+	if len(edits) != expectedCount {
+		t.Errorf("Expected %d edits, got %d", expectedCount, len(edits))
+		for _, e := range edits {
+			t.Logf("Edit: %s at %d", e.NewText, e.Range.Start.Line)
+		}
+	}
+
+	// Check Implicit Signal Rename
+	foundImplicit := false
+	for _, e := range edits {
+		if e.Range.Start.Line == 11 {
+			if e.NewText == "NewSig" {
+				foundImplicit = true
+			}
+		}
+	}
+	if !foundImplicit {
+		t.Error("Did not find implicit signal rename")
+	}
+
+	// Check Alias Rename
+	foundAlias := false
+	for _, e := range edits {
+		if e.Range.Start.Line == 13 {
+			// Alias = Sig1. Range should cover Sig1.
+			if e.NewText == "NewSig" {
+				foundAlias = true
+			}
+		}
+	}
+	if !foundAlias {
+		t.Error("Did not find alias reference rename")
+	}
+}
diff --git a/test/lsp_rename_test.go b/test/lsp_rename_test.go
new file mode 100644
index 0000000..13690c1
--- /dev/null
+++ b/test/lsp_rename_test.go
@@ -0,0 +1,92 @@
+package integration
+
+import (
+	"testing"
+
+	"github.com/marte-community/marte-dev-tools/internal/index"
+	"github.com/marte-community/marte-dev-tools/internal/lsp"
+	"github.com/marte-community/marte-dev-tools/internal/parser"
+)
+
+func TestHandleRename(t *testing.T) {
+	// Setup
+	lsp.Tree = index.NewProjectTree()
+	lsp.Documents = make(map[string]string)
+
+	content := `
+#package Some
++MyNode = {
+    Class = Type
+}
++Consumer = {
+    Link = MyNode
+    PkgLink = Some.MyNode
+}
+`
+	uri := "file://rename.marte"
+	lsp.Documents[uri] = content
+	p := parser.NewParser(content)
+	cfg, err := p.Parse()
+	if err != nil {
+		t.Fatal(err)
+	}
+	lsp.Tree.AddFile("rename.marte", cfg)
+	lsp.Tree.ResolveReferences()
+
+	// Rename +MyNode to NewNode
+	// +MyNode is at Line 2 (after #package)
+	// Line 0: empty
+	// Line 1: #package
+	// Line 2: +MyNode
+	params := lsp.RenameParams{
+		TextDocument: lsp.TextDocumentIdentifier{URI: uri},
+		Position:     lsp.Position{Line: 2, Character: 4}, // +MyNode
+		NewName:      "NewNode",
+	}
+
+	edit := lsp.HandleRename(params)
+	if edit == nil {
+		t.Fatal("Expected edits")
+	}
+
+	edits := edit.Changes[uri]
+	if len(edits) != 3 {
+		t.Errorf("Expected 3 edits (Def, Link, PkgLink), got %d", len(edits))
+	}
+
+	// Verify Definition change (+MyNode -> +NewNode)
+	foundDef := false
+	for _, e := range edits {
+		if e.NewText == "+NewNode" {
+			foundDef = true
+			if e.Range.Start.Line != 2 {
+				t.Errorf("Definition edit line wrong: %d", e.Range.Start.Line)
+			}
+		}
+	}
+	if !foundDef {
+		t.Error("Did not find definition edit +NewNode")
+	}
+
+	// Verify Link change (MyNode -> NewNode)
+	foundLink := false
+	for _, e := range edits {
+		if e.NewText == "NewNode" && e.Range.Start.Line == 6 { // Link = MyNode
+			foundLink = true
+		}
+	}
+	if !foundLink {
+		t.Error("Did not find Link edit")
+	}
+
+	// Verify PkgLink change (Some.MyNode -> Some.NewNode)
+	foundPkg := false
+	for _, e := range edits {
+		if e.NewText == "NewNode" && e.Range.Start.Line == 7 { // PkgLink = Some.MyNode
+			foundPkg = true
+		}
+	}
+	if !foundPkg {
+		t.Error("Did not find PkgLink edit")
+	}
+}
diff --git a/test/validator_multifile_test.go b/test/validator_multifile_test.go
index 1f1fc23..5b1c833 100644
--- a/test/validator_multifile_test.go
+++ b/test/validator_multifile_test.go
@@ -107,7 +107,11 @@ func TestHierarchicalPackageMerge(t *testing.T) {
 	}
 
 	// We can also inspect the tree to verify FieldX is there (optional, but good for confidence)
-	baseNode := idx.Root.Children["Base"]
+	projNode := idx.Root.Children["Proj"]
+	if projNode == nil {
+		t.Fatal("Proj node not found")
+	}
+	baseNode := projNode.Children["Base"]
 	if baseNode == nil {
 		t.Fatal("Base node not found")
 	}