fix: preserve generated app registrations

internal/bootstrap/bootstrap.go

@@ -479,12 +479,34 @@ func renderPlatformDeliveryConfig(dir string, cfg config.Config) error {
 
 func copyAndRenderPlatformDeliveryBases(templateDir, repoDir string, cfg config.Config) error {
 	bases := []string{"gateway", "tekton", "tekton-triggers"}
+	apps := filepath.Join(repoDir, "base", "tekton", "apps")
+	backup := apps + ".maidn-preserve"
+	if err := os.RemoveAll(backup); err != nil {
+		return err
+	}
+	if _, err := os.Stat(apps); err == nil {
+		if err := os.Rename(apps, backup); err != nil {
+			return err
+		}
+	} else if !os.IsNotExist(err) {
+		return err
+	}
 	for _, base := range bases {
 		baseDir := filepath.Join(repoDir, "base", base)
 		if err := copyDir(filepath.Join(templateDir, "base", base), baseDir, true); err != nil {
 			return err
 		}
 	}
+	if _, err := os.Stat(backup); err == nil {
+		if err := os.RemoveAll(apps); err != nil {
+			return err
+		}
+		if err := os.Rename(backup, apps); err != nil {
+			return err
+		}
+	} else if !os.IsNotExist(err) {
+		return err
+	}
 	for _, base := range bases {
 		baseDir := filepath.Join(repoDir, "base", base)
 		if err := renderPlatformDeliveryConfig(baseDir, cfg); err != nil {

internal/bootstrap/bootstrap_test.go

@@ -240,6 +240,13 @@ func TestCopyAndRenderPlatformDeliveryBasesOverwritesExistingMigrationOutput(t *
 	if err := os.WriteFile(customGatewayFile, []byte("custom: route\n"), 0644); err != nil {
 		t.Fatal(err)
 	}
+	appRegistration := filepath.Join(repoDir, "base", "tekton", "apps", "fixture.yaml")
+	if err := os.MkdirAll(filepath.Dir(appRegistration), 0755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(appRegistration, []byte("registered: fixture\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
 
 	cfg := config.Config{
 		Git:       config.GitConfig{BaseURL: "https://git.example.test", Owner: "user-org"},
@@ -259,6 +266,10 @@ func TestCopyAndRenderPlatformDeliveryBasesOverwritesExistingMigrationOutput(t *
 	if err != nil || string(content) != "custom: route\n" {
 		t.Fatalf("custom gateway file was not preserved: %q, %v", content, err)
 	}
+	content, err = os.ReadFile(appRegistration)
+	if err != nil || string(content) != "registered: fixture\n" {
+		t.Fatalf("generated app registration was not preserved: %q, %v", content, err)
+	}
 }
 
 func TestCopyTemplateBaseComponentsRefreshesCNPGAndPreservesGeneratedSecrets(t *testing.T) {