diff --git a/src/resources/extensions/gsd/guided-flow.ts b/src/resources/extensions/gsd/guided-flow.ts
index a62ec2504..5cb6503a5 100644
--- a/src/resources/extensions/gsd/guided-flow.ts
+++ b/src/resources/extensions/gsd/guided-flow.ts
@@ -85,6 +85,7 @@ interface PendingAutoStartEntry {
   basePath: string;
   milestoneId: string; // the milestone being discussed
   step?: boolean; // preserve step mode through discuss → auto transition
+  createdAt: number; // timestamp for staleness detection (#3274)
 }
 
 const pendingAutoStartMap = new Map<string, PendingAutoStartEntry>();
@@ -104,8 +105,8 @@ function _getPendingAutoStart(basePath?: string): PendingAutoStartEntry | null {
  * Store pending auto-start state for a project.
  * Exported for testing (#2985).
  */
-export function setPendingAutoStart(basePath: string, entry: { basePath: string; milestoneId: string; ctx?: ExtensionCommandContext; pi?: ExtensionAPI; step?: boolean }): void {
-  pendingAutoStartMap.set(basePath, entry as PendingAutoStartEntry);
+export function setPendingAutoStart(basePath: string, entry: { basePath: string; milestoneId: string; ctx?: ExtensionCommandContext; pi?: ExtensionAPI; step?: boolean; createdAt?: number }): void {
+  pendingAutoStartMap.set(basePath, { createdAt: Date.now(), ...entry } as PendingAutoStartEntry);
 }
 
 /**
@@ -460,7 +461,7 @@ export async function showHeadlessMilestoneCreation(
   const prompt = buildHeadlessDiscussPrompt(nextId, seedContext, basePath);
 
   // Set pending auto start (auto-mode triggers on "Milestone X ready." via checkAutoStartAfterDiscuss)
-  pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId });
+  pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, createdAt: Date.now() });
 
   // Dispatch — headless milestone creation is a planning activity
   await dispatchWorkflow(pi, prompt, "gsd-run", ctx, "plan-milestone");
@@ -640,12 +641,12 @@ export async function showDiscuss(
       const seed = draftContent
         ? `${basePrompt}\n\n## Prior Discussion (Draft Seed)\n\n${draftContent}`
         : basePrompt;
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: mid, step: false });
+      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: mid, step: false, createdAt: Date.now() });
       await dispatchWorkflow(pi, seed, "gsd-discuss", ctx, "discuss-milestone");
     } else if (choice === "discuss_fresh") {
       const discussMilestoneTemplates = inlineTemplate("context", "Context");
       const structuredQuestionsAvailable = pi.getActiveTools().includes("ask_user_questions") ? "true" : "false";
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: mid, step: false });
+      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: mid, step: false, createdAt: Date.now() });
       await dispatchWorkflow(pi, loadPrompt("guided-discuss-milestone", {
         milestoneId: mid, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
         commitInstruction: buildDocsCommitInstruction(`docs(${mid}): milestone context from discuss`),
@@ -654,7 +655,7 @@ export async function showDiscuss(
       const milestoneIds = findMilestoneIds(basePath);
       const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
       const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: false });
+      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: false, createdAt: Date.now() });
       await dispatchWorkflow(pi, buildDiscussPrompt(nextId, `New milestone ${nextId}.`, basePath), "gsd-run", ctx, "discuss-milestone");
     }
     return;
@@ -1016,7 +1017,7 @@ async function handleMilestoneActions(
     const milestoneIds = findMilestoneIds(basePath);
     const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
     const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
-    pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
+    pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
     await dispatchWorkflow(pi, buildDiscussPrompt(nextId,
       `New milestone ${nextId}.`,
       basePath
@@ -1144,14 +1145,15 @@ export async function showSmartEntry(
     // and fires another dispatchWorkflow, resetting the conversation mid-interview.
     if (pendingAutoStartMap.has(basePath)) {
       // #3274: If /clear interrupted the discussion, the pending entry is stale.
-      // Detect this by checking if the discussion manifest still exists — it's
-      // only present while a discuss flow is actively in progress.
-      const manifestExists = existsSync(join(gsdRoot(basePath), "DISCUSSION-MANIFEST.json"));
+      // Detect staleness: no manifest, no CONTEXT.md, AND entry is older than
+      // 30s (avoids race between .set() and LLM writing first artifact).
       const entry = pendingAutoStartMap.get(basePath)!;
+      const ageMs = Date.now() - (entry.createdAt || 0);
+      const manifestExists = existsSync(join(gsdRoot(basePath), "DISCUSSION-MANIFEST.json"));
       const milestoneHasContext = existsSync(
         join(gsdRoot(basePath), "milestones", entry.milestoneId, `${entry.milestoneId}-CONTEXT.md`),
       );
-      if (!manifestExists && !milestoneHasContext) {
+      if (!manifestExists && !milestoneHasContext && ageMs > 30_000) {
         // Stale entry from an interrupted discussion — clear and continue
         pendingAutoStartMap.delete(basePath);
       } else {
@@ -1188,7 +1190,7 @@ export async function showSmartEntry(
 
     if (isFirst) {
       // First ever — skip wizard, just ask directly
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
+      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
       await dispatchWorkflow(pi, buildDiscussPrompt(nextId,
         `New project, milestone ${nextId}. Do NOT read or explore .gsd/ — it's empty scaffolding.`,
         basePath
@@ -1209,7 +1211,7 @@ export async function showSmartEntry(
       });
 
       if (choice === "new_milestone") {
-        pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
+        pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
         await dispatchWorkflow(pi, buildDiscussPrompt(nextId,
           `New milestone ${nextId}.`,
           basePath
@@ -1248,7 +1250,7 @@ export async function showSmartEntry(
       const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
       const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
 
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
+      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
       await dispatchWorkflow(pi, buildDiscussPrompt(nextId,
         `New milestone ${nextId}.`,
         basePath
@@ -1299,12 +1301,12 @@ export async function showSmartEntry(
       const seed = draftContent
         ? `${basePrompt}\n\n## Prior Discussion (Draft Seed)\n\n${draftContent}`
         : basePrompt;
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode });
+      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode, createdAt: Date.now() });
       await dispatchWorkflow(pi, seed, "gsd-discuss", ctx, "discuss-milestone");
     } else if (choice === "discuss_fresh") {
       const discussMilestoneTemplates = inlineTemplate("context", "Context");
       const structuredQuestionsAvailable = pi.getActiveTools().includes("ask_user_questions") ? "true" : "false";
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode });
+      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode, createdAt: Date.now() });
       await dispatchWorkflow(pi, loadPrompt("guided-discuss-milestone", {
         milestoneId, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
         commitInstruction: buildDocsCommitInstruction(`docs(${milestoneId}): milestone context from discuss`),
@@ -1313,7 +1315,7 @@ export async function showSmartEntry(
       const milestoneIds = findMilestoneIds(basePath);
       const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
       const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
+      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
       await dispatchWorkflow(pi, buildDiscussPrompt(nextId,
         `New milestone ${nextId}.`,
         basePath
@@ -1366,7 +1368,7 @@ export async function showSmartEntry(
       });
 
       if (choice === "plan") {
-        pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode });
+        pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode, createdAt: Date.now() });
         const planMilestoneTemplates = [
           inlineTemplate("roadmap", "Roadmap"),
           inlineTemplate("plan", "Slice Plan"),
@@ -1397,7 +1399,7 @@ export async function showSmartEntry(
         const milestoneIds = findMilestoneIds(basePath);
         const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
         const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
-        pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
+        pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
         await dispatchWorkflow(pi, buildDiscussPrompt(nextId,
           `New milestone ${nextId}.`,
           basePath