fix(extract): keep committed palette skeletons out of stale cleanup (#96)

Extract skips writing *palcus.itp back to source (build projects them from blueprints, #50), but the skip branch never marked the skeleton target as desired, so cleanupStaleFiles deleted the committed source/palettes/*.itp.json on every extract — shipping modules with empty custom palettes. Fix marks the skipped target desired; regression test builds a module with a committed skeleton and asserts extract leaves it in place.

🤖 Generated with [Claude Code](https://claude.com/claude-code)Reviewed-on: #96

Co-authored-by: vickydotbat <vickydotbat@tutamail.com>

internal/pipeline/pipeline_test.go

@@ -3312,6 +3312,88 @@ func TestExtractOverwritesAndRemovesStaleFiles(t *testing.T) {
 	}
 }
 
+func TestExtractKeepsPaletteSkeletonsThroughStaleCleanup(t *testing.T) {
+	root := t.TempDir()
+	mustMkdir(t, filepath.Join(root, "src", "module"))
+	mustMkdir(t, filepath.Join(root, "src", "palettes"))
+	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"
+      }
+    ]
+  }
+}
+`)
+	skeletonPath := filepath.Join(root, "src", "palettes", "creaturepalcus.itp.json")
+	mustWriteFile(t, skeletonPath, `{
+  "file_type": "ITP ",
+  "file_version": "V3.2",
+  "root": {
+    "struct_type": 0,
+    "fields": [
+      {
+        "label": "MAIN",
+        "type": "List",
+        "value": []
+      }
+    ]
+  }
+}
+`)
+
+	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 := 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.Removed != 0 {
+		t.Fatalf("expected no removed files, got %d", result.Removed)
+	}
+	if _, err := os.Stat(skeletonPath); err != nil {
+		t.Fatalf("expected palette skeleton to survive extract, stat err=%v", err)
+	}
+}
+
 func TestExtractMergesConfiguredGFFJSONFieldsAndLists(t *testing.T) {
 	root := t.TempDir()
 	mustMkdir(t, filepath.Join(root, "src", "module"))