feat(runtime): forward Flynn prompt to pi and harden backend mode commands

src/backends/piEmbedded.test.ts

@@ -60,6 +60,54 @@ describe('PiEmbeddedBackend', () => {
     }
   });
 
+  it('injects Flynn system prompt fields into session payload in hybrid mode', async () => {
+    const mod = createModule(`
+      export function createAgentSession() {
+        return {
+          run(payload) {
+            return { text: payload.systemPrompt ?? payload.system ?? "missing" };
+          },
+        };
+      }
+    `);
+
+    try {
+      const backend = new PiEmbeddedBackend({ module: mod.moduleUrl, timeoutMs: 2000, systemPromptMode: 'hybrid' });
+      const result = await backend.process({
+        prompt: 'hello',
+        history: [],
+        systemPrompt: 'SOUL + IDENTITY + USER + TOOLS',
+      });
+      expect(result).toBe('SOUL + IDENTITY + USER + TOOLS');
+    } finally {
+      mod.cleanup();
+    }
+  });
+
+  it('omits Flynn system prompt injection in pi_default mode', async () => {
+    const mod = createModule(`
+      export function createAgentSession() {
+        return {
+          run(payload) {
+            return { text: payload.systemPrompt ? "present" : "absent" };
+          },
+        };
+      }
+    `);
+
+    try {
+      const backend = new PiEmbeddedBackend({ module: mod.moduleUrl, timeoutMs: 2000, systemPromptMode: 'pi_default' });
+      const result = await backend.process({
+        prompt: 'hello',
+        history: [],
+        systemPrompt: 'should not be forwarded',
+      });
+      expect(result).toBe('absent');
+    } finally {
+      mod.cleanup();
+    }
+  });
+
   it('throws when module has no supported session factory', async () => {
     const mod = createModule('export const version = "0.0.0";');
 
@@ -100,6 +148,35 @@ describe('PiEmbeddedBackend', () => {
     }
   });
 
+  it('applies Flynn system prompt in Agent runtime via setSystemPrompt()', async () => {
+    const mod = createModule(`
+      export class Agent {
+        constructor() {
+          this.systemPrompt = "";
+          this.state = { messages: [] };
+        }
+        setSystemPrompt(prompt) {
+          this.systemPrompt = prompt;
+        }
+        async prompt(input) {
+          this.state.messages.push({ role: "assistant", content: [{ type: "text", text: this.systemPrompt + " :: " + input }] });
+        }
+      }
+    `);
+
+    try {
+      const backend = new PiEmbeddedBackend({ module: mod.moduleUrl, timeoutMs: 2000, systemPromptMode: 'flynn' });
+      const result = await backend.process({
+        prompt: 'hello',
+        history: [],
+        systemPrompt: 'use flynn prompt',
+      });
+      expect(result).toBe('use flynn prompt :: hello');
+    } finally {
+      mod.cleanup();
+    }
+  });
+
   it('surfaces agent state error when no assistant text is produced', async () => {
     const mod = createModule(`
       export class Agent {