fix(coding-agent): make config env references explicit

closes #5095

packages/coding-agent/src/utils/deprecation.ts

@@ -0,0 +1,14 @@
+import chalk from "chalk";
+
+const emittedDeprecationWarnings = new Set<string>();
+
+export function warnDeprecation(message: string): void {
+	if (emittedDeprecationWarnings.has(message)) return;
+	emittedDeprecationWarnings.add(message);
+	console.warn(chalk.yellow(`Deprecation warning: ${message}`));
+}
+
+/** Clear deprecation warning state. Exported for tests. */
+export function clearDeprecationWarningsForTests(): void {
+	emittedDeprecationWarnings.clear();
+}

packages/coding-agent/src/utils/json.ts

@@ -0,0 +1,6 @@
+/** Strip `//` line comments and trailing commas from JSON, leaving string literals untouched. */
+export function stripJsonComments(input: string): string {
+	return input
+		.replace(/"(?:\\.|[^"\\])*"|\/\/[^\n]*/g, (m) => (m[0] === '"' ? m : ""))
+		.replace(/"(?:\\.|[^"\\])*"|,(\s*[}\]])/g, (m, tail) => tail ?? (m[0] === '"' ? m : ""));
+}