fix(runner) preserve native instructions (#1557)

* fix(codex): preserve native instructions

Keep HAPI guidance in the developer layer so app-server retains Codex persistence rules. Align long-running goal states with the Codex 0.147 protocol.

* fix(codex): filter new goal statuses

cli/src/codex/utils/appServerConfig.test.ts

@@ -15,6 +15,29 @@ describe('appServerConfig', () => {
         return `${developerInstructions}\n\n${codexCollaborationSpawnAgentInstructions}`;
     };
 
+    it('preserves Codex built-in base instructions by omitting the default override', () => {
+        const params = buildThreadStartParams({
+            cwd: '/workspace/project',
+            mode: { permissionMode: 'default', collaborationMode: 'default' },
+            mcpServers
+        });
+
+        expect(params).not.toHaveProperty('baseInstructions');
+        expect(params.developerInstructions).toBe(codexSystemPrompt);
+    });
+
+    it('keeps an explicit base instruction override separate from HAPI developer instructions', () => {
+        const params = buildThreadStartParams({
+            cwd: '/workspace/project',
+            mode: { permissionMode: 'default', collaborationMode: 'default' },
+            mcpServers,
+            baseInstructions: 'Custom base instructions.'
+        });
+
+        expect(params.baseInstructions).toBe('Custom base instructions.');
+        expect(params.developerInstructions).toBe(codexSystemPrompt);
+    });
+
     it('applies CLI overrides when permission mode is default', () => {
         const params = buildThreadStartParams({
             cwd: '/workspace/project',
@@ -26,7 +49,7 @@ describe('appServerConfig', () => {
         expect(params.cwd).toBe('/workspace/project');
         expect(params.sandbox).toBe('danger-full-access');
         expect(params.approvalPolicy).toBe('never');
-        expect(params.baseInstructions).toBe(codexSystemPrompt);
+        expect(params.baseInstructions).toBeUndefined();
         expect(params.developerInstructions).toBe(codexSystemPrompt);
         expect(params.config).toEqual({
             'mcp_servers.hapi': {
@@ -129,7 +152,7 @@ describe('appServerConfig', () => {
         });
     });
 
-    it('concatenates custom developer instructions after base instructions', () => {
+    it('concatenates custom developer instructions after HAPI instructions without overriding base instructions', () => {
         const params = buildThreadStartParams({
             cwd: '/workspace/project',
             mode: { permissionMode: 'default', collaborationMode: 'default' },
@@ -137,7 +160,7 @@ describe('appServerConfig', () => {
             developerInstructions: 'Only respond in Chinese.'
         });
 
-        expect(params.baseInstructions).toBe(codexSystemPrompt);
+        expect(params.baseInstructions).toBeUndefined();
         expect(params.developerInstructions).toBe(`${codexSystemPrompt}\n\nOnly respond in Chinese.`);
         expect(params.config).toEqual({
             'mcp_servers.hapi': {

cli/src/codex/utils/appServerConfig.ts

@@ -114,11 +114,12 @@ function buildMcpServerConfig(mcpServers: McpServersConfig): Record<string, unkn
 function resolveInstructions(args: {
     baseInstructions?: string;
     developerInstructions?: string;
-}): { baseInstructions: string; developerInstructions: string } {
-    const baseInstructions = args.baseInstructions ?? getCodexSystemPrompt();
+}): { baseInstructions: string | undefined; developerInstructions: string } {
+    const baseInstructions = args.baseInstructions;
+    const hapiDeveloperInstructions = getCodexSystemPrompt();
     const developerInstructions = args.developerInstructions
-        ? `${baseInstructions}\n\n${args.developerInstructions}`
-        : baseInstructions;
+        ? `${hapiDeveloperInstructions}\n\n${args.developerInstructions}`
+        : hapiDeveloperInstructions;
     return {
         baseInstructions,
         developerInstructions
@@ -218,7 +219,7 @@ export function buildThreadStartParams(args: {
         cwd: args.cwd,
         approvalPolicy: resolvedApprovalPolicy,
         sandbox: resolvedSandbox,
-        baseInstructions,
+        ...(baseInstructions !== undefined ? { baseInstructions } : {}),
         developerInstructions: resolvedDeveloperInstructions,
         ...(Object.keys(configWithInstructions).length > 0 ? { config: configWithInstructions } : {})
     };