diff --git a/internal/app/app.go b/internal/app/app.go
index a5bb5c5..f5467be 100644
--- a/internal/app/app.go
+++ b/internal/app/app.go
@@ -181,6 +181,8 @@ func runExtract(ctx context) error {
 		fmt.Fprintf(ctx.stdout, "hak archives: %d\n", len(result.HAKPaths))
 	}
 	fmt.Fprintf(ctx.stdout, "written: %d\n", result.Written)
+	fmt.Fprintf(ctx.stdout, "overwritten: %d\n", result.Overwritten)
+	fmt.Fprintf(ctx.stdout, "removed: %d\n", result.Removed)
 	fmt.Fprintf(ctx.stdout, "skipped: %d\n", result.Skipped)
 	return nil
 }
diff --git a/internal/pipeline/build.go b/internal/pipeline/build.go
index d9246ff..b951427 100644
--- a/internal/pipeline/build.go
+++ b/internal/pipeline/build.go
@@ -269,7 +269,7 @@ func resourceFromJSON(path string, moduleHakOrder []string) (erf.Resource, error
 	}
 
 	return erf.Resource{
-		Name: name,
+		Name: strings.ToLower(name),
 		Type: resourceType,
 		Data: buf.Bytes(),
 	}, nil
@@ -281,7 +281,7 @@ func pathResource(path string) (erf.Resource, error) {
 	if !ok {
 		return erf.Resource{}, fmt.Errorf("unsupported resource extension %q", filepath.Ext(path))
 	}
-	name := strings.TrimSuffix(filepath.Base(path), filepath.Ext(path))
+	name := strings.ToLower(strings.TrimSuffix(filepath.Base(path), filepath.Ext(path)))
 	info, err := os.Stat(path)
 	if err != nil {
 		return erf.Resource{}, fmt.Errorf("stat %s: %w", path, err)
@@ -300,13 +300,13 @@ func rawResource(path string) (erf.Resource, error) {
 	if !ok {
 		return erf.Resource{}, fmt.Errorf("unsupported resource extension %q", filepath.Ext(path))
 	}
-	name := strings.TrimSuffix(filepath.Base(path), filepath.Ext(path))
+	name := strings.ToLower(strings.TrimSuffix(filepath.Base(path), filepath.Ext(path)))
 	data, err := os.ReadFile(path)
 	if err != nil {
 		return erf.Resource{}, fmt.Errorf("read %s: %w", path, err)
 	}
 	return erf.Resource{
-		Name: name,
+		Name: strings.ToLower(name),
 		Type: resourceType,
 		Data: data,
 	}, nil
@@ -322,7 +322,7 @@ func splitSourceName(path string) (string, string, error) {
 	if extension == "" {
 		return "", "", fmt.Errorf("source file must include target resource extension before .json: %s", path)
 	}
-	return strings.TrimSuffix(stem, extension), strings.ToLower(extension), nil
+	return strings.ToLower(strings.TrimSuffix(stem, extension)), strings.ToLower(extension), nil
 }
 
 func planHAKChunks(p *project.Project, assets []assetResource) ([]hakChunk, error) {
diff --git a/internal/pipeline/extract.go b/internal/pipeline/extract.go
index 55e82f3..a752e68 100644
--- a/internal/pipeline/extract.go
+++ b/internal/pipeline/extract.go
@@ -16,10 +16,12 @@ import (
 )
 
 type ExtractResult struct {
-	ModulePath string
-	HAKPaths   []string
-	Written    int
-	Skipped    int
+	ModulePath  string
+	HAKPaths    []string
+	Written     int
+	Overwritten int
+	Removed     int
+	Skipped     int
 }
 
 func Extract(p *project.Project) (ExtractResult, error) {
@@ -38,9 +40,11 @@ func Extract(p *project.Project) (ExtractResult, error) {
 	var result ExtractResult
 	result.ModulePath = modulePath
 	var failures []error
+	desired := map[string]struct{}{}
 
-	written, skipped, errs := extractArchiveResources(p, archive)
+	written, overwritten, skipped, errs := extractArchiveResources(p, archive, desired)
 	result.Written += written
+	result.Overwritten += overwritten
 	result.Skipped += skipped
 	failures = append(failures, errs...)
 
@@ -63,21 +67,27 @@ func Extract(p *project.Project) (ExtractResult, error) {
 		}
 
 		result.HAKPaths = append(result.HAKPaths, hakPath)
-		written, skipped, errs := extractArchiveResources(p, hakArchive)
+		written, overwritten, skipped, errs := extractArchiveResources(p, hakArchive, desired)
 		result.Written += written
+		result.Overwritten += overwritten
 		result.Skipped += skipped
 		failures = append(failures, errs...)
 	}
 
+	removed, errs := cleanupStaleFiles(p, desired)
+	result.Removed = removed
+	failures = append(failures, errs...)
+
 	if len(failures) > 0 {
 		return result, errors.Join(failures...)
 	}
 	return result, nil
 }
 
-func extractArchiveResources(p *project.Project, archive erf.Archive) (int, int, []error) {
+func extractArchiveResources(p *project.Project, archive erf.Archive, desired map[string]struct{}) (int, int, int, []error) {
 	var failures []error
 	writtenCount := 0
+	overwrittenCount := 0
 	skippedCount := 0
 
 	for _, resource := range archive.Resources {
@@ -86,20 +96,24 @@ func extractArchiveResources(p *project.Project, archive erf.Archive) (int, int,
 			failures = append(failures, err)
 			continue
 		}
+		desired[target] = struct{}{}
 
-		written, err := writeSafely(target, data)
+		state, err := writeManagedFile(target, data)
 		if err != nil {
 			failures = append(failures, err)
 			continue
 		}
-		if written {
+		switch state {
+		case writeNew:
 			writtenCount++
-		} else {
+		case writeOverwritten:
+			overwrittenCount++
+		case writeSkipped:
 			skippedCount++
 		}
 	}
 
-	return writtenCount, skippedCount, failures
+	return writtenCount, overwrittenCount, skippedCount, failures
 }
 
 func extractedFile(p *project.Project, resource erf.Resource) (string, []byte, error) {
@@ -107,10 +121,11 @@ func extractedFile(p *project.Project, resource erf.Resource) (string, []byte, e
 	if !ok {
 		return "", nil, fmt.Errorf("unsupported resource type 0x%04X for %s", resource.Type, resource.Name)
 	}
+	resref := strings.ToLower(resource.Name)
 
 	switch extension {
 	case "nss":
-		return filepath.Join(p.SourceDir(), "scripts", resource.Name+".nss"), resource.Data, nil
+		return filepath.Join(p.SourceDir(), "scripts", resref+".nss"), resource.Data, nil
 	case "utc", "utd", "ute", "uti", "utm", "utp", "uts", "utt", "utw",
 		"are", "dlg", "fac", "gic", "git", "ifo", "itp", "jrl":
 		document, err := gff.Read(bytes.NewReader(resource.Data))
@@ -122,32 +137,96 @@ func extractedFile(p *project.Project, resource erf.Resource) (string, []byte, e
 			return "", nil, fmt.Errorf("marshal json %s.%s: %w", resource.Name, extension, err)
 		}
 		formatted = append(formatted, '\n')
-		return filepath.Join(p.SourceDir(), sourceSubdir(extension), resource.Name+"."+extension+".json"), formatted, nil
+		return filepath.Join(p.SourceDir(), sourceSubdir(extension), resref+"."+extension+".json"), formatted, nil
 	default:
-		return filepath.Join(p.AssetsDir(), extension, resource.Name+"."+extension), resource.Data, nil
+		return filepath.Join(p.AssetsDir(), extension, resref+"."+extension), resource.Data, nil
 	}
 }
 
-func writeSafely(path string, data []byte) (bool, error) {
+type writeState int
+
+const (
+	writeSkipped writeState = iota
+	writeNew
+	writeOverwritten
+)
+
+func writeManagedFile(path string, data []byte) (writeState, error) {
 	if err := os.MkdirAll(filepath.Dir(path), 0o755); err != nil {
-		return false, fmt.Errorf("create parent directory for %s: %w", path, err)
+		return writeSkipped, fmt.Errorf("create parent directory for %s: %w", path, err)
 	}
 
 	existing, err := os.ReadFile(path)
 	if err == nil {
 		if bytes.Equal(existing, data) {
-			return false, nil
+			return writeSkipped, nil
 		}
-		return false, fmt.Errorf("refusing to overwrite existing file with different contents: %s", path)
+		if err := os.WriteFile(path, data, 0o644); err != nil {
+			return writeSkipped, fmt.Errorf("overwrite %s: %w", path, err)
+		}
+		return writeOverwritten, nil
 	}
 	if !errors.Is(err, os.ErrNotExist) {
-		return false, fmt.Errorf("check existing file %s: %w", path, err)
+		return writeSkipped, fmt.Errorf("check existing file %s: %w", path, err)
 	}
 
 	if err := os.WriteFile(path, data, 0o644); err != nil {
-		return false, fmt.Errorf("write %s: %w", path, err)
+		return writeSkipped, fmt.Errorf("write %s: %w", path, err)
+	}
+	return writeNew, nil
+}
+
+func cleanupStaleFiles(p *project.Project, desired map[string]struct{}) (int, []error) {
+	candidates := make([]string, 0, len(p.Inventory.SourceFiles)+len(p.Inventory.ScriptFiles)+len(p.Inventory.AssetFiles))
+	for _, rel := range p.Inventory.SourceFiles {
+		candidates = append(candidates, filepath.Join(p.SourceDir(), filepath.FromSlash(rel)))
+	}
+	for _, rel := range p.Inventory.ScriptFiles {
+		candidates = append(candidates, filepath.Join(p.SourceDir(), filepath.FromSlash(rel)))
+	}
+	for _, rel := range p.Inventory.AssetFiles {
+		candidates = append(candidates, filepath.Join(p.AssetsDir(), filepath.FromSlash(rel)))
+	}
+
+	removed := 0
+	var failures []error
+	for _, path := range candidates {
+		if _, keep := desired[path]; keep {
+			continue
+		}
+		if err := os.Remove(path); err != nil {
+			if errors.Is(err, os.ErrNotExist) {
+				continue
+			}
+			failures = append(failures, fmt.Errorf("remove stale file %s: %w", path, err))
+			continue
+		}
+		removed++
+		cleanupEmptyParents(filepath.Dir(path), p.SourceDir(), p.AssetsDir())
+	}
+	return removed, failures
+}
+
+func cleanupEmptyParents(dir string, roots ...string) {
+	for {
+		if dir == "." || dir == string(filepath.Separator) {
+			return
+		}
+		stop := false
+		for _, root := range roots {
+			if dir == root {
+				stop = true
+				break
+			}
+		}
+		if stop {
+			return
+		}
+		if err := os.Remove(dir); err != nil {
+			return
+		}
+		dir = filepath.Dir(dir)
 	}
-	return true, nil
 }
 
 func sourceSubdir(extension string) string {
diff --git a/internal/pipeline/pipeline_test.go b/internal/pipeline/pipeline_test.go
index 1b8b47d..cac2964 100644
--- a/internal/pipeline/pipeline_test.go
+++ b/internal/pipeline/pipeline_test.go
@@ -607,6 +607,172 @@ func TestBuildSkipsEmptyHAKGroupsInModuleOrder(t *testing.T) {
 	}
 }
 
+func TestExtractOverwritesAndRemovesStaleFiles(t *testing.T) {
+	root := t.TempDir()
+	mustMkdir(t, filepath.Join(root, "src", "module"))
+	mustMkdir(t, filepath.Join(root, "src", "areas"))
+	mustMkdir(t, filepath.Join(root, "assets"))
+	mustMkdir(t, filepath.Join(root, "build"))
+
+	mustWriteFile(t, filepath.Join(root, "nwn-tool.json"), `{
+  "module": {
+    "name": "Test Module",
+    "resref": "testmod"
+  },
+  "paths": {
+    "source": "src",
+    "assets": "assets",
+    "build": "build"
+  }
+}
+`)
+
+	mustWriteFile(t, filepath.Join(root, "src", "module", "module.ifo.json"), `{
+  "file_type": "IFO ",
+  "file_version": "V3.2",
+  "root": {
+    "struct_type": 0,
+    "fields": [
+      {
+        "label": "Mod_Name",
+        "type": "CExoString",
+        "value": "Original Module"
+      }
+    ]
+  }
+}
+`)
+
+	p, err := project.Load(root)
+	if err != nil {
+		t.Fatalf("load project: %v", err)
+	}
+	if err := p.ValidateLayout(); err != nil {
+		t.Fatalf("validate layout: %v", err)
+	}
+	if err := p.Scan(); err != nil {
+		t.Fatalf("scan: %v", err)
+	}
+
+	if _, err := BuildModule(p); err != nil {
+		t.Fatalf("build module: %v", err)
+	}
+
+	mustWriteFile(t, filepath.Join(root, "src", "module", "module.ifo.json"), `{
+  "file_type": "IFO ",
+  "file_version": "V3.2",
+  "root": {
+    "struct_type": 0,
+    "fields": [
+      {
+        "label": "Mod_Name",
+        "type": "CExoString",
+        "value": "Changed In Toolset"
+      }
+    ]
+  }
+}
+`)
+	mustWriteFile(t, filepath.Join(root, "src", "areas", "area001.are.json"), `{"stale": true}`)
+
+	if err := p.Scan(); err != nil {
+		t.Fatalf("rescan before extract: %v", err)
+	}
+
+	result, err := Extract(p)
+	if err != nil {
+		t.Fatalf("extract: %v", err)
+	}
+	if result.Overwritten != 1 {
+		t.Fatalf("expected 1 overwritten file, got %d", result.Overwritten)
+	}
+	if result.Removed != 1 {
+		t.Fatalf("expected 1 removed stale file, got %d", result.Removed)
+	}
+
+	raw, err := os.ReadFile(filepath.Join(root, "src", "module", "module.ifo.json"))
+	if err != nil {
+		t.Fatalf("read extracted module file: %v", err)
+	}
+	if !strings.Contains(string(raw), "Original Module") {
+		t.Fatalf("expected extracted module file to be overwritten with archive contents:\n%s", string(raw))
+	}
+	if _, err := os.Stat(filepath.Join(root, "src", "areas", "area001.are.json")); !os.IsNotExist(err) {
+		t.Fatalf("expected stale area file to be removed, stat err=%v", err)
+	}
+}
+
+func TestExtractNormalizesResourceNamesToLowercase(t *testing.T) {
+	root := t.TempDir()
+	mustMkdir(t, filepath.Join(root, "src", "blueprints", "items"))
+	mustMkdir(t, filepath.Join(root, "assets"))
+	mustMkdir(t, filepath.Join(root, "build"))
+
+	mustWriteFile(t, filepath.Join(root, "nwn-tool.json"), `{
+  "module": {
+    "name": "Test Module",
+    "resref": "testmod"
+  },
+  "paths": {
+    "source": "src",
+    "assets": "assets",
+    "build": "build"
+  }
+}
+`)
+
+	mustWriteFile(t, filepath.Join(root, "src", "blueprints", "items", "I_ELVENCHAIN.uti.json"), `{
+  "file_type": "UTI ",
+  "file_version": "V3.2",
+  "root": {
+    "struct_type": 0,
+    "fields": [
+      {
+        "label": "LocalizedName",
+        "type": "CExoString",
+        "value": "Elven Chain"
+      }
+    ]
+  }
+}
+`)
+
+	p, err := project.Load(root)
+	if err != nil {
+		t.Fatalf("load project: %v", err)
+	}
+	if err := p.ValidateLayout(); err != nil {
+		t.Fatalf("validate layout: %v", err)
+	}
+	if err := p.Scan(); err != nil {
+		t.Fatalf("scan: %v", err)
+	}
+
+	if _, err := BuildModule(p); err != nil {
+		t.Fatalf("build module: %v", err)
+	}
+	if err := os.Remove(filepath.Join(root, "src", "blueprints", "items", "I_ELVENCHAIN.uti.json")); err != nil {
+		t.Fatalf("remove uppercase source file: %v", err)
+	}
+	if err := p.Scan(); err != nil {
+		t.Fatalf("rescan before extract: %v", err)
+	}
+
+	result, err := Extract(p)
+	if err != nil {
+		t.Fatalf("extract: %v", err)
+	}
+	if result.Written != 1 {
+		t.Fatalf("expected 1 written file, got %d", result.Written)
+	}
+	if _, err := os.Stat(filepath.Join(root, "src", "blueprints", "items", "i_elvenchain.uti.json")); err != nil {
+		t.Fatalf("expected lowercase extracted resource: %v", err)
+	}
+	if _, err := os.Stat(filepath.Join(root, "src", "blueprints", "items", "I_ELVENCHAIN.uti.json")); !os.IsNotExist(err) {
+		t.Fatalf("expected uppercase extracted resource path to be absent, stat err=%v", err)
+	}
+}
+
 func mustMkdir(t *testing.T, path string) {
 	t.Helper()
 	if err := os.MkdirAll(path, 0o755); err != nil {
diff --git a/internal/validator/validator.go b/internal/validator/validator.go
index b6c303c..ca08515 100644
--- a/internal/validator/validator.go
+++ b/internal/validator/validator.go
@@ -76,6 +76,9 @@ func ValidateProject(p *project.Project) Report {
 	resolver := newAssetGroupResolver(p)
 
 	for _, rel := range p.Inventory.SourceFiles {
+		if hasUppercaseResourceName(rel) {
+			report.add(rel, "resource filenames should be lowercase", SeverityWarning)
+		}
 		abs := filepath.Join(p.SourceDir(), filepath.FromSlash(rel))
 		document, resref, extension, err := loadDocument(abs)
 		if err != nil {
@@ -90,7 +93,7 @@ func ValidateProject(p *project.Project) Report {
 			Document:  document,
 		})
 
-		key := resref + "." + extension
+		key := strings.ToLower(resref) + "." + extension
 		if previous, exists := resourceIndex[key]; exists {
 			report.add(rel, fmt.Sprintf("duplicate resource %s also defined by %s", key, previous), SeverityError)
 		} else {
@@ -101,7 +104,10 @@ func ValidateProject(p *project.Project) Report {
 	}
 
 	for _, rel := range p.Inventory.ScriptFiles {
-		base := strings.TrimSuffix(filepath.Base(rel), filepath.Ext(rel))
+		if hasUppercaseResourceName(rel) {
+			report.add(rel, "resource filenames should be lowercase", SeverityWarning)
+		}
+		base := strings.ToLower(strings.TrimSuffix(filepath.Base(rel), filepath.Ext(rel)))
 		if previous, exists := scriptIndex[base]; exists {
 			report.add(rel, fmt.Sprintf("duplicate script resource %s also defined by %s", base, previous), SeverityError)
 		} else {
@@ -110,9 +116,12 @@ func ValidateProject(p *project.Project) Report {
 	}
 
 	for _, rel := range p.Inventory.AssetFiles {
-		base := strings.TrimSuffix(filepath.Base(rel), filepath.Ext(rel))
+		if hasUppercaseResourceName(rel) {
+			report.add(rel, "resource filenames should be lowercase", SeverityWarning)
+		}
+		base := strings.ToLower(strings.TrimSuffix(filepath.Base(rel), filepath.Ext(rel)))
 		extension := strings.TrimPrefix(strings.ToLower(filepath.Ext(rel)), ".")
-		key := base + "." + extension
+		key := strings.ToLower(base) + "." + extension
 		if _, exists := assetIndex[key]; !exists {
 			assetIndex[key] = rel
 		}
@@ -187,7 +196,7 @@ func loadDocument(path string) (gff.Document, string, string, error) {
 	if extension == "" {
 		return gff.Document{}, "", "", fmt.Errorf("missing resource extension before .json")
 	}
-	resref := strings.TrimSuffix(stem, "."+extension)
+	resref := strings.ToLower(strings.TrimSuffix(stem, "."+extension))
 
 	var document gff.Document
 	if err := json.Unmarshal(raw, &document); err != nil {
@@ -250,25 +259,25 @@ func validateReferences(report *Report, document loadedDocument, resources, scri
 			if isBuiltinScript(value) {
 				return
 			}
-			if _, exists := scripts[value]; !exists {
+			if _, exists := scripts[strings.ToLower(value)]; !exists {
 				report.add(document.Path, fmt.Sprintf("missing script reference %q from field %q", value, field.Label), SeverityError)
 			}
 		case field.Label == "Conversation":
-			key := value + ".dlg"
+			key := strings.ToLower(value) + ".dlg"
 			if _, exists := resources[key]; !exists {
 				report.add(document.Path, fmt.Sprintf("missing dialog reference %q", key), SeverityError)
 			}
 		case field.Label == "Mod_Entry_Area":
-			key := value + ".are"
+			key := strings.ToLower(value) + ".are"
 			if _, exists := resources[key]; !exists {
 				report.add(document.Path, fmt.Sprintf("missing area reference %q", key), SeverityError)
 			}
 		case field.Label == "Model":
-			if !hasAsset(value, []string{"mdl"}, assets) {
+			if !hasAsset(strings.ToLower(value), []string{"mdl"}, assets) {
 				report.add(document.Path, fmt.Sprintf("missing model asset for %q", value), SeverityError)
 			}
 		case field.Label == "Sound":
-			if !hasAsset(value, []string{"wav"}, assets) {
+			if !hasAsset(strings.ToLower(value), []string{"wav"}, assets) {
 				report.add(document.Path, fmt.Sprintf("missing sound asset for %q", value), SeverityError)
 			}
 		}
@@ -390,6 +399,11 @@ func walkFields(s gff.Struct, visit func(gff.Field)) {
 	}
 }
 
+func hasUppercaseResourceName(rel string) bool {
+	base := filepath.Base(rel)
+	return base != strings.ToLower(base)
+}
+
 func fieldStringValue(value gff.Value) (string, bool) {
 	switch typed := value.(type) {
 	case gff.StringValue:
diff --git a/internal/validator/validator_test.go b/internal/validator/validator_test.go
index 76bf94b..e4e6b3c 100644
--- a/internal/validator/validator_test.go
+++ b/internal/validator/validator_test.go
@@ -54,6 +54,49 @@ func TestValidateProjectWarnsForCrossHAKDuplicateAssets(t *testing.T) {
 	}
 }
 
+func TestValidateProjectWarnsForUppercaseResourceNames(t *testing.T) {
+	root := t.TempDir()
+	mustMkdir(t, filepath.Join(root, "src", "blueprints", "items"))
+	mustMkdir(t, filepath.Join(root, "assets", "vfx"))
+	mustMkdir(t, filepath.Join(root, "build"))
+
+	mustWriteFile(t, filepath.Join(root, "nwn-tool.json"), `{
+  "module": {
+    "name": "Test Module",
+    "resref": "testmod"
+  },
+  "paths": {
+    "source": "src",
+    "assets": "assets",
+    "build": "build"
+  }
+}
+`)
+	mustWriteFile(t, filepath.Join(root, "src", "blueprints", "items", "I_ELVENCHAIN.uti.json"), `{
+  "file_type": "UTI ",
+  "file_version": "V3.2",
+  "root": {"struct_type": 0, "fields": []}
+}
+`)
+	mustWriteFile(t, filepath.Join(root, "assets", "vfx", "SPELL_FIRE.tga"), "fire")
+
+	p, err := project.Load(root)
+	if err != nil {
+		t.Fatalf("load project: %v", err)
+	}
+	if err := p.ValidateLayout(); err != nil {
+		t.Fatalf("validate layout: %v", err)
+	}
+	if err := p.Scan(); err != nil {
+		t.Fatalf("scan: %v", err)
+	}
+
+	report := ValidateProject(p)
+	if report.WarningCount() < 2 {
+		t.Fatalf("expected lowercase warnings, got %#v", report.Diagnostics)
+	}
+}
+
 func mustMkdir(t *testing.T, path string) {
 	t.Helper()
 	if err := os.MkdirAll(path, 0o755); err != nil {