diff --git a/src/resources/extensions/gsd/gitignore.ts b/src/resources/extensions/gsd/gitignore.ts
index 3d6a52c74..8626bc6af 100644
--- a/src/resources/extensions/gsd/gitignore.ts
+++ b/src/resources/extensions/gsd/gitignore.ts
@@ -23,6 +23,7 @@ const BASELINE_PATTERNS = [
   ".gsd/metrics.json",
   ".gsd/completed-units.json",
   ".gsd/STATE.md",
+  ".gsd/DISCUSSION-MANIFEST.json",
 
   // ── OS junk ──
   ".DS_Store",
diff --git a/src/resources/extensions/gsd/guided-flow.ts b/src/resources/extensions/gsd/guided-flow.ts
index d85c31862..fddd76d6f 100644
--- a/src/resources/extensions/gsd/guided-flow.ts
+++ b/src/resources/extensions/gsd/guided-flow.ts
@@ -50,13 +50,76 @@ export function checkAutoStartAfterDiscuss(): boolean {
 
   const { ctx, pi, basePath, milestoneId, step } = pendingAutoStart;
 
-  // Don't fire until the discuss phase has actually produced a context file
-  // for the milestone being discussed. agent_end fires after every LLM turn,
-  // including the initial "What do you want to build?" response — we need to
-  // wait for the full conversation to complete and the LLM to write CONTEXT.md.
+  // Gate 1: Primary milestone must have CONTEXT.md
   const contextFile = resolveMilestoneFile(basePath, milestoneId, "CONTEXT");
   if (!contextFile) return false; // no context yet — keep waiting
 
+  // Gate 2: STATE.md must exist — written as the last step in the discuss
+  // output phase. This prevents auto-start from firing during Phase 3
+  // (sequential readiness gates for remaining milestones) in multi-milestone
+  // discussions, where M001-CONTEXT.md exists but M002/M003 haven't been
+  // processed yet.
+  const stateFile = resolveGsdRootFile(basePath, "STATE");
+  if (!stateFile) return false; // discussion not finalized yet
+
+  // Gate 3: Multi-milestone completeness warning
+  // Parse PROJECT.md for milestone sequence, warn if any are missing context.
+  // Don't block — milestones can be intentionally queued without context.
+  const projectFile = resolveGsdRootFile(basePath, "PROJECT");
+  if (projectFile) {
+    try {
+      const projectContent = readFileSync(projectFile, "utf-8");
+      const milestoneIds = parseMilestoneSequenceFromProject(projectContent);
+      if (milestoneIds.length > 1) {
+        const missing = milestoneIds.filter(id => {
+          const hasContext = !!resolveMilestoneFile(basePath, id, "CONTEXT");
+          const hasDraft = !!resolveMilestoneFile(basePath, id, "CONTEXT-DRAFT");
+          const hasDir = existsSync(join(basePath, ".gsd", "milestones", id));
+          return !hasContext && !hasDraft && !hasDir;
+        });
+        if (missing.length > 0) {
+          ctx.ui.notify(
+            `Multi-milestone validation: ${missing.join(", ")} not found in filesystem. ` +
+            `Discussion may not have completed all readiness gates.`,
+            "warning",
+          );
+        }
+      }
+    } catch { /* non-fatal — PROJECT.md parsing failure shouldn't block auto-start */ }
+  }
+
+  // Gate 4: Discussion manifest process verification (multi-milestone only)
+  // The LLM writes DISCUSSION-MANIFEST.json after each Phase 3 gate decision.
+  // If the manifest exists but gates_completed < total, the LLM hasn't finished
+  // presenting all readiness gates to the user — block auto-start.
+  const manifestPath = join(basePath, ".gsd", "DISCUSSION-MANIFEST.json");
+  if (existsSync(manifestPath)) {
+    try {
+      const manifest = JSON.parse(readFileSync(manifestPath, "utf-8"));
+      const total = typeof manifest.total === "number" ? manifest.total : 0;
+      const completed = typeof manifest.gates_completed === "number" ? manifest.gates_completed : 0;
+
+      if (total > 1 && completed < total) {
+        // Discussion not complete — block auto-start until all gates are done
+        return false;
+      }
+
+      // Cross-check manifest milestones against PROJECT.md if available
+      if (projectFile) {
+        const projectContent = readFileSync(projectFile, "utf-8");
+        const projectIds = parseMilestoneSequenceFromProject(projectContent);
+        const manifestIds = Object.keys(manifest.milestones ?? {});
+        const untracked = projectIds.filter(id => !manifestIds.includes(id));
+        if (untracked.length > 0) {
+          ctx.ui.notify(
+            `Discussion manifest missing gates for: ${untracked.join(", ")}`,
+            "warning",
+          );
+        }
+      }
+    } catch { /* malformed manifest — warn but don't block */ }
+  }
+
   // Draft promotion cleanup: if a CONTEXT-DRAFT.md exists alongside the new
   // CONTEXT.md, delete the draft — it's been consumed by the discussion.
   try {
@@ -64,11 +127,28 @@ export function checkAutoStartAfterDiscuss(): boolean {
     if (draftFile) unlinkSync(draftFile);
   } catch { /* non-fatal — stale draft doesn't break anything, CONTEXT.md wins */ }
 
+  // Cleanup: remove discussion manifest after auto-start (only needed during discussion)
+  try { unlinkSync(manifestPath); } catch { /* may not exist for single-milestone */ }
+
   pendingAutoStart = null;
   startAuto(ctx, pi, basePath, false, { step }).catch(() => {});
   return true;
 }
 
+/**
+ * Extract milestone IDs from PROJECT.md milestone sequence table.
+ * Looks for rows like "| M001 | Name | Status |" and extracts the ID column.
+ */
+function parseMilestoneSequenceFromProject(content: string): string[] {
+  const ids: string[] = [];
+  const lines = content.split(/\r?\n/);
+  for (const line of lines) {
+    const match = line.match(/^\|\s*(M\d{3}[A-Z0-9-]*)\s*\|/);
+    if (match) ids.push(match[1]);
+  }
+  return ids;
+}
+
 // ─── Types ────────────────────────────────────────────────────────────────────
 
 type UIContext = ExtensionContext;
diff --git a/src/resources/extensions/gsd/prompts/discuss.md b/src/resources/extensions/gsd/prompts/discuss.md
index accdbc8ce..fef9176b8 100644
--- a/src/resources/extensions/gsd/prompts/discuss.md
+++ b/src/resources/extensions/gsd/prompts/discuss.md
@@ -227,6 +227,27 @@ For each remaining milestone **one at a time, in sequence**, use `ask_user_quest
 
 Each context file (full or draft) should be rich enough that a future agent encountering it fresh — with no memory of this conversation — can understand the intent, constraints, dependencies, what this milestone unlocks, and what "done" looks like.
 
+#### Milestone Gate Tracking (MANDATORY for multi-milestone)
+
+After EVERY Phase 3 gate decision, immediately write or update `.gsd/DISCUSSION-MANIFEST.json` with the cumulative state. This file is mechanically validated by the system before auto-mode starts — if gates are incomplete, auto-mode will NOT start.
+
+```json
+{
+  "primary": "M001",
+  "milestones": {
+    "M001": { "gate": "discussed", "context": "full" },
+    "M002": { "gate": "discussed", "context": "full" },
+    "M003": { "gate": "queued",    "context": "none" }
+  },
+  "total": 3,
+  "gates_completed": 3
+}
+```
+
+Write this file AFTER each gate decision, not just at the end. Update `gates_completed` incrementally. The system reads this file and BLOCKS auto-start if `gates_completed < total`.
+
+For single-milestone projects, do NOT write this file — it is only for multi-milestone discussions.
+
 #### Phase 4: Finalize
 
 7. Update `.gsd/STATE.md`
diff --git a/src/resources/extensions/gsd/tests/draft-promotion.test.ts b/src/resources/extensions/gsd/tests/draft-promotion.test.ts
index 4ea6f976c..0ce24ed50 100644
--- a/src/resources/extensions/gsd/tests/draft-promotion.test.ts
+++ b/src/resources/extensions/gsd/tests/draft-promotion.test.ts
@@ -145,7 +145,8 @@ const guidedFlowSource = readFileSync(
 );
 
 const checkFnIdx = guidedFlowSource.indexOf("checkAutoStartAfterDiscuss");
-const checkFnChunk = guidedFlowSource.slice(checkFnIdx, checkFnIdx + 1200);
+const checkFnEnd = guidedFlowSource.indexOf("\nexport ", checkFnIdx + 1);
+const checkFnChunk = guidedFlowSource.slice(checkFnIdx, checkFnEnd > checkFnIdx ? checkFnEnd : checkFnIdx + 5000);
 
 assert(
   checkFnChunk.includes("CONTEXT-DRAFT"),