fix: Append memFS system prompt based on CLI flags (#840)

src/headless.ts

@@ -669,6 +669,20 @@ export async function handleHeadlessCommand(
     settingsManager.setMemfsEnabled(agent.id, true);
   }
 
+  // Ensure agent's system prompt includes/excludes memfs section to match setting
+  if (
+    memfsFlag ||
+    noMemfsFlag ||
+    (isNewlyCreatedAgent && !isSubagent) ||
+    (specifiedAgentId && !isSubagent)
+  ) {
+    const { updateAgentSystemPromptMemfs } = await import("./agent/modify");
+    await updateAgentSystemPromptMemfs(
+      agent.id,
+      settingsManager.isMemfsEnabled(agent.id),
+    );
+  }
+
   // Sync filesystem-backed memory before creating conversations (only if memfs is enabled)
   if (settingsManager.isMemfsEnabled(agent.id)) {
     try {

src/index.ts

@@ -1649,6 +1649,17 @@ async function main(): Promise<void> {
           settingsManager.setMemfsEnabled(agent.id, true);
         }
 
+        // Ensure agent's system prompt includes/excludes memfs section to match setting
+        if (memfsFlag || noMemfsFlag || (isNewlyCreatedAgent && !isSubagent)) {
+          const { updateAgentSystemPromptMemfs } = await import(
+            "./agent/modify"
+          );
+          await updateAgentSystemPromptMemfs(
+            agent.id,
+            settingsManager.isMemfsEnabled(agent.id),
+          );
+        }
+
         // Fire-and-forget: Initialize loaded skills flag (LET-7101)
         // Don't await - this is just for the skill unload reminder
         initializeLoadedSkillsFlag().catch(() => {