Keep runtime provider overrides on overlay refresh

packages/coding-agent/src/config/model-registry.ts

@@ -1672,6 +1672,16 @@ export class ModelRegistry {
 			compat: override.compat ? mergeCompat(baseOverride?.compat, override.compat) : baseOverride?.compat,
 		};
 	}
+	#applyProviderTransportOverride<T extends { baseUrl?: string; headers?: Record<string, string> }>(
+		entry: T,
+		override: Pick<ProviderOverride, "baseUrl" | "headers">,
+	): T {
+		return {
+			...entry,
+			baseUrl: override.baseUrl ?? entry.baseUrl,
+			headers: override.headers ? { ...entry.headers, ...override.headers } : entry.headers,
+		};
+	}
 	#applyModelOverrides(models: Model<Api>[], overrides: Map<string, Map<string, ModelOverride>>): Model<Api>[] {
 		if (overrides.size === 0) return models;
 		return models.map(model => {
@@ -2075,18 +2085,19 @@ export class ModelRegistry {
 		}
 
 		if (config.baseUrl || config.headers) {
-			const nextRuntimeOverride = this.#mergeProviderOverride(this.#runtimeProviderOverrides.get(providerName), {
-				baseUrl: config.baseUrl,
-				headers: config.headers,
-			});
+			const transportOverride = { baseUrl: config.baseUrl, headers: config.headers };
+			const nextRuntimeOverride = this.#mergeProviderOverride(
+				this.#runtimeProviderOverrides.get(providerName),
+				transportOverride,
+			);
 			this.#runtimeProviderOverrides.set(providerName, nextRuntimeOverride);
+			this.#runtimeModelOverlays = this.#runtimeModelOverlays.map(overlay => {
+				if (overlay.provider !== providerName) return overlay;
+				return this.#applyProviderTransportOverride(overlay, transportOverride);
+			});
 			this.#models = this.#models.map(m => {
 				if (m.provider !== providerName) return m;
-				return {
-					...m,
-					baseUrl: config.baseUrl ?? m.baseUrl,
-					headers: config.headers ? { ...m.headers, ...config.headers } : m.headers,
-				};
+				return this.#applyProviderTransportOverride(m, transportOverride);
 			});
 			this.#rebuildCanonicalIndex();
 		}

packages/coding-agent/test/model-registry-runtime-provider.test.ts

@@ -261,6 +261,49 @@ describe("ModelRegistry runtime provider registration", () => {
 		expect(model?.api).toBe("openai-completions");
 	});
 
+	test("runtime model overlays keep provider overrides across refresh cycles", async () => {
+		const registry = new ModelRegistry(authStorage, modelsJsonPath);
+		const runtimeHeader = "X-Runtime-Overlay-Header";
+		const overrideBaseUrl = "https://runtime-overridden.example.com/v1";
+		const modelId = "runtime-override-survivor";
+
+		registry.registerProvider(
+			"runtime-provider",
+			{
+				baseUrl: "https://runtime.example.com/v1",
+				apiKey: "RUNTIME_KEY",
+				api: "openai-completions",
+				models: [{ ...baseModel, id: modelId }],
+			},
+			"ext://runtime",
+		);
+		registry.registerProvider(
+			"runtime-provider",
+			{ baseUrl: overrideBaseUrl, headers: { [runtimeHeader]: "runtime-header" } },
+			"ext://runtime",
+		);
+
+		const modelAfterOverride = registry.find("runtime-provider", modelId);
+		expect(modelAfterOverride).toBeDefined();
+		expect(modelAfterOverride?.baseUrl).toBe(overrideBaseUrl);
+		expect(modelAfterOverride?.headers?.[runtimeHeader]).toBe("runtime-header");
+
+		await registry.refresh("offline");
+		const modelAfterRefresh = registry.find("runtime-provider", modelId);
+		expect(modelAfterRefresh).toBeDefined();
+		expect(modelAfterRefresh?.baseUrl).toBe(overrideBaseUrl);
+		expect(modelAfterRefresh?.headers?.[runtimeHeader]).toBe("runtime-header");
+
+		await registry.refreshProvider("runtime-provider", "offline");
+		const modelAfterProviderRefresh = registry.find("runtime-provider", modelId);
+		expect(modelAfterProviderRefresh).toBeDefined();
+		expect(modelAfterProviderRefresh?.baseUrl).toBe(overrideBaseUrl);
+		expect(modelAfterProviderRefresh?.headers?.[runtimeHeader]).toBe("runtime-header");
+
+		registry.clearSourceRegistrations("ext://runtime");
+		expect(registry.find("runtime-provider", modelId)).toBeUndefined();
+	});
+
 	test("extension-registered API keys survive refresh cycle for auth resolution", async () => {
 		const registry = new ModelRegistry(authStorage, modelsJsonPath);