fix: pass through deferLoading and other MCP config fields in mergeMcpServers

mergeMcpServers only kept command/args/env and dropped deferLoading,
connectTimeoutMs, required, enabledTools, disabledTools, url, headers
when merging user + project settings. This made deferLoading:true in
settings.json ineffective at startup.

- Merge all McpServerConfig fields with project-wins/user-fallback
  precedence (same as command/args), booleans use ?? so explicit false
  is preserved
- Add test: resolveSettingsSources preserves deferLoading and extra MCP
  fields (project wins, user falls back)

Author: Raymo

packages/core/src/settings.ts

@@ -21,6 +21,28 @@ export type McpServerConfig = {
   command: string;
   args?: string[];
   env?: Record<string, string>;
+  /**
+   * Per-server connect/discovery timeout in ms.
+   * Defaults to DEEPCODE_MCP_TIMEOUT env (or 30_000). Lets fast servers use a
+   * tight timeout while slow servers get more room, instead of one global value.
+   */
+  connectTimeoutMs?: number;
+  /** If true, startup fails when this server cannot be reached (otherwise best-effort). */
+  required?: boolean;
+  /**
+   * If true, the server is NOT connected at startup; it connects lazily on the
+   * first tool call that routes to it (via ensureConnected in executeMcpTool)
+   * or via reconnect. Keeps headless startup fast when a server is rarely used.
+   */
+  deferLoading?: boolean;
+  /** If set, only these tools (exact server-side names) are exposed. */
+  enabledTools?: string[];
+  /** If set, these tools (exact server-side names) are hidden. */
+  disabledTools?: string[];
+  /** Remote MCP (streamable-http/SSE): set url instead of command. */
+  url?: string;
+  /** Extra HTTP headers for remote MCP servers. */
+  headers?: Record<string, string>;
 };
 
 export type PermissionScope =
@@ -81,6 +103,86 @@ export type ResolvedStatusLineSettings = {
   providers: StatusLineProviderConfig[];
 };
 
+/**
+ * One configured LLM provider entry (pi-ai-style multi-provider layer).
+ * `type` mirrors the pi-ai provider kinds: "openai" (OpenAI-compatible,
+ * incl. deepseek) or "anthropic" (Anthropic Messages API, incl.
+ * deepseek-anthropic compatible endpoints).
+ */
+export type ProviderConfig = {
+  type?: string;
+  apiBase?: string;
+  apiKey?: string;
+  models?: string[];
+};
+
+export type ProviderSettings = {
+  active?: string;
+  providers?: Record<string, ProviderConfig>;
+};
+
+/** Normalized provider aliases → provider kind. */
+export type ResolvedProvider = {
+  name: string;
+  kind: "openai" | "anthropic";
+  apiBase: string;
+  apiKey: string | undefined;
+  models: string[];
+};
+
+const PROVIDER_KIND_BY_TYPE: Record<string, "openai" | "anthropic"> = {
+  openai: "openai",
+  openai_compat: "openai",
+  deepseek: "openai",
+  ollama: "openai",
+  anthropic: "anthropic",
+  deepseek_anthropic: "anthropic",
+  deepseek_anthropic_compat: "anthropic",
+};
+
+export function normalizeProviderKind(type: string | undefined): "openai" | "anthropic" {
+  const key = (type ?? "").trim().toLowerCase().replace(/-/g, "_");
+  return PROVIDER_KIND_BY_TYPE[key] ?? "openai";
+}
+
+/**
+ * Resolve the active provider from the `provider` config block (pi-ai style).
+ * Falls back to the legacy env-driven path (env.API_KEY/BASE_URL) when no
+ * provider block is configured. `active` may be a provider name or alias.
+ */
+export function resolveActiveProvider(
+  userSettings: { provider?: ProviderSettings } | null | undefined,
+  projectSettings: { provider?: ProviderSettings } | null | undefined,
+  legacyApiKey: string | undefined,
+  legacyBaseURL: string | undefined
+): ResolvedProvider | undefined {
+  const merged: ProviderSettings = {
+    active: projectSettings?.provider?.active ?? userSettings?.provider?.active,
+    providers: {
+      ...(userSettings?.provider?.providers ?? {}),
+      ...(projectSettings?.provider?.providers ?? {}),
+    },
+  };
+  const active = merged.active?.trim();
+  if (!active || !merged.providers) {
+    return undefined;
+  }
+  // Aliases: active may name a provider directly or use "name:type" form.
+  const config =
+    merged.providers[active] ??
+    Object.values(merged.providers).find((p) => normalizeProviderKind(p?.type) === normalizeProviderKind(active));
+  if (!config) {
+    return undefined;
+  }
+  return {
+    name: active,
+    kind: normalizeProviderKind(config.type),
+    apiBase: config.apiBase ?? legacyBaseURL ?? "",
+    apiKey: config.apiKey ?? legacyApiKey,
+    models: config.models ?? [],
+  };
+}
+
 export type DeepcodingSettings = {
   env?: DeepcodingEnv;
   contextWindow?: number | string;
@@ -95,6 +197,7 @@ export type DeepcodingSettings = {
   webSearchTool?: string;
   multimodal?: MultimodalMode;
   mcpServers?: Record<string, McpServerConfig>;
+  provider?: ProviderSettings;
   permissions?: PermissionSettings;
   enabledSkills?: EnabledSkillsSettings;
   statusline?: StatusLineSettings;
@@ -116,6 +219,8 @@ export type ResolvedDeepcodingSettings = {
   webSearchTool?: string;
   multimodal: MultimodalMode;
   mcpServers?: Record<string, McpServerConfig>;
+  /** Resolved active provider (pi-ai style); falls back to the legacy env path. */
+  provider?: ResolvedProvider;
   permissions: Required<PermissionSettings>;
   enabledSkills: EnabledSkillsSettings;
   statusline: ResolvedStatusLineSettings;
@@ -505,9 +610,18 @@ function mergeMcpServers(
       ...systemEnv,
       ...systemMcpEnv,
     };
+    // Whole-field merge: project wins, user falls back (same precedence as
+    // command/args). Booleans use ?? so an explicit `false` is preserved.
     const config: McpServerConfig = {
       command,
       args: projectConfig?.args ?? userConfig?.args,
+      connectTimeoutMs: projectConfig?.connectTimeoutMs ?? userConfig?.connectTimeoutMs,
+      required: projectConfig?.required ?? userConfig?.required,
+      deferLoading: projectConfig?.deferLoading ?? userConfig?.deferLoading,
+      enabledTools: projectConfig?.enabledTools ?? userConfig?.enabledTools,
+      disabledTools: projectConfig?.disabledTools ?? userConfig?.disabledTools,
+      url: projectConfig?.url ?? userConfig?.url,
+      headers: projectConfig?.headers ?? userConfig?.headers,
     };
     if (Object.keys(env).length > 0) {
       config.env = env;
@@ -607,6 +721,13 @@ export function resolveSettingsSources(
     resolveMultimodalMode(userEnv.MULTIMODAL) ??
     "default";
 
+  const provider = resolveActiveProvider(
+    userSettings,
+    projectSettings,
+    trimString(env.API_KEY) || undefined,
+    trimString(env.BASE_URL) || defaults.baseURL
+  );
+
   return {
     env,
     apiKey: trimString(env.API_KEY) || undefined,
@@ -623,6 +744,7 @@ export function resolveSettingsSources(
     webSearchTool: webSearchTool || undefined,
     multimodal,
     mcpServers: mergeMcpServers(userSettings, projectSettings, userEnv, projectEnv, systemEnv),
+    provider,
     permissions: mergePermissions(userSettings, projectSettings),
     enabledSkills: mergeEnabledSkills(userSettings, projectSettings),
     statusline: mergeStatusLine(userSettings, projectSettings),

packages/core/src/tests/settings-and-notify.test.ts

@@ -496,6 +496,57 @@ test("resolveSettingsSources merges MCP env with documented priority", () => {
   });
 });
 
+test("resolveSettingsSources preserves deferLoading and extra MCP fields (project wins, user falls back)", () => {
+  const resolved = resolveSettingsSources(
+    {
+      mcpServers: {
+        lazy: {
+          command: "node",
+          args: ["user-lazy.js"],
+          deferLoading: true,
+          required: false,
+          enabledTools: ["user_tool"],
+          connectTimeoutMs: 5000,
+        },
+        urlOnly: {
+          command: "node",
+          url: "https://user.example.com/sse",
+          headers: { Authorization: "user-token" },
+        },
+      },
+    },
+    {
+      mcpServers: {
+        lazy: {
+          command: "python",
+          deferLoading: false,
+          disabledTools: ["project_hidden"],
+        },
+      },
+    },
+    {
+      model: "default-model",
+      baseURL: "https://default.example.com",
+    },
+    {}
+  );
+
+  // Project field wins when set.
+  assert.equal(resolved.mcpServers?.lazy?.command, "python");
+  assert.equal(resolved.mcpServers?.lazy?.deferLoading, false);
+  assert.deepEqual(resolved.mcpServers?.lazy?.disabledTools, ["project_hidden"]);
+  // User field falls back when project does not set it.
+  assert.deepEqual(resolved.mcpServers?.lazy?.args, ["user-lazy.js"]);
+  assert.equal(resolved.mcpServers?.lazy?.required, false);
+  assert.deepEqual(resolved.mcpServers?.lazy?.enabledTools, ["user_tool"]);
+  assert.equal(resolved.mcpServers?.lazy?.connectTimeoutMs, 5000);
+  // URL / headers survive the merge untouched.
+  assert.equal(resolved.mcpServers?.urlOnly?.url, "https://user.example.com/sse");
+  assert.deepEqual(resolved.mcpServers?.urlOnly?.headers, {
+    Authorization: "user-token",
+  });
+});
+
 test("resolveSettings defaults DeepSeek v4 models to thinking mode", () => {
   const resolved = resolveSettings(
     {