Fix fetcher rendering empty fields

internal/cmd/fetcher/main.go

@@ -294,8 +294,8 @@ func runPluginTests(ctx context.Context, logger *slog.Logger, plugins []createdP
 }
 
 // updatePluginDeps updates plugin dependencies in a buf.plugin.yaml file to their latest versions.
-// It parses the YAML content, finds any entries in the "deps:" section with "plugin:" fields,
-// and updates them to use the latest available version from latestVersions map.
+// It parses the YAML content to find deps entries, then uses text replacement to update
+// version references in-place, preserving the original formatting and comments.
 // For example, if the YAML contains:
 //
 //	deps:
@@ -320,9 +320,10 @@ func updatePluginDeps(ctx context.Context, logger *slog.Logger, content []byte,
 		return content, nil
 	}
 
-	modified := false
-	for i := range config.Deps {
-		dep := &config.Deps[i]
+	// Use text replacement rather than re-marshaling the struct to avoid introducing
+	// empty fields from zero-value nested structs in ExternalConfig.
+	result := string(content)
+	for _, dep := range config.Deps {
 		if dep.Plugin == "" {
 			continue
 		}
@@ -334,27 +335,18 @@ func updatePluginDeps(ctx context.Context, logger *slog.Logger, content []byte,
 		}
 
 		// Look up the latest version for this plugin
-		if latestVersion, exists := latestVersions[pluginName]; exists && latestVersion != currentVersion {
-			oldPluginRef := dep.Plugin
-			newPluginRef := pluginName + ":" + latestVersion
-			dep.Plugin = newPluginRef
-			logger.InfoContext(ctx, "updating plugin dependency", slog.String("old", oldPluginRef), slog.String("new", newPluginRef))
-			modified = true
+		latestVersion, exists := latestVersions[pluginName]
+		if !exists || latestVersion == currentVersion {
+			continue
 		}
-	}
-
-	if !modified {
-		// No changes made, return original content
-		return content, nil
-	}
 
-	// Marshal back to YAML
-	updatedContent, err := encoding.MarshalYAML(&config)
-	if err != nil {
-		return nil, fmt.Errorf("failed to marshal updated YAML: %w", err)
+		oldPluginRef := dep.Plugin
+		newPluginRef := pluginName + ":" + latestVersion
+		logger.InfoContext(ctx, "updating plugin dependency", slog.String("old", oldPluginRef), slog.String("new", newPluginRef))
+		result = strings.ReplaceAll(result, oldPluginRef, newPluginRef)
 	}
 
-	return updatedContent, nil
+	return []byte(result), nil
 }
 
 // pluginToCreate represents a plugin that needs a new version created.

internal/cmd/fetcher/main_test.go

@@ -103,6 +103,44 @@ plugin_version: v1.0.0
 		},
 	}
 
+	// Regression test: updating deps must not re-marshal the full config, which would
+	// introduce empty fields for zero-value nested structs and strip YAML comments.
+	t.Run("preserves formatting and comments without adding empty fields", func(t *testing.T) {
+		t.Parallel()
+		input := `version: v1
+name: buf.build/test/grpc-go
+plugin_version: v1.5.1
+deps:
+  - plugin: buf.build/protocolbuffers/go:v1.35.0
+registry:
+  go:
+    # https://pkg.go.dev/google.golang.org/grpc
+    min_version: "1.21"
+    deps:
+      - module: google.golang.org/grpc
+        version: v1.70.0
+  opts:
+    - paths=source_relative
+`
+		latestVersions := map[string]string{
+			"buf.build/protocolbuffers/go": "v1.36.11",
+		}
+		logger := slog.New(slog.NewTextHandler(testWriter{t}, &slog.HandlerOptions{Level: slog.LevelDebug}))
+		result, err := updatePluginDeps(t.Context(), logger, []byte(input), latestVersions)
+		require.NoError(t, err)
+
+		output := string(result)
+		// Dep version should be updated.
+		assert.Contains(t, output, "buf.build/protocolbuffers/go:v1.36.11")
+		// Comment in the registry section should be preserved.
+		assert.Contains(t, output, "# https://pkg.go.dev/google.golang.org/grpc")
+		// No empty fields should have been introduced.
+		assert.NotContains(t, output, "npm:")
+		assert.NotContains(t, output, "maven:")
+		assert.NotContains(t, output, "source_url: \"\"")
+		assert.NotContains(t, output, "description: \"\"")
+	})
+
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
 			t.Parallel()