gsd-pi 2.78.1 → 2.79.0

package/src/resources/extensions/gsd/guided-flow.ts

@@ -10,11 +10,18 @@ import type { ExtensionAPI, ExtensionContext, ExtensionCommandContext } from "@g
 import type { GSDState } from "./types.js";
 import { showNextAction } from "../shared/tui.js";
 import { loadFile, saveFile } from "./files.js";
-import { isDbAvailable, getMilestoneSlices } from "./gsd-db.js";
+import { isDbAvailable, getMilestone, getMilestoneSlices } from "./gsd-db.js";
 import { parseRoadmapSlices } from "./roadmap-slices.js";
 import { loadPrompt, inlineTemplate } from "./prompt-loader.js";
-import { buildDiscussMilestonePrompt, buildSkillActivationBlock } from "./auto-prompts.js";
-import { deriveState } from "./state.js";
+import {
+  buildCompleteSlicePrompt,
+  buildDiscussMilestonePrompt,
+  buildExecuteTaskPrompt,
+  buildPlanMilestonePrompt,
+  buildPlanSlicePrompt,
+  buildSkillActivationBlock,
+} from "./auto-prompts.js";
+import { deriveState, isGhostMilestone } from "./state.js";
 import { invalidateAllCaches } from "./cache.js";
 import { startAutoDetached } from "./auto.js";
 import { clearLock } from "./crash-recovery.js";
@@ -25,15 +32,16 @@ import {
 } from "./interrupted-session.js";
 import { listUnitRuntimeRecords, clearUnitRuntimeRecord } from "./unit-runtime.js";
 import { resolveExpectedArtifactPath } from "./auto.js";
+import { gsdHome } from "./gsd-home.js";
 import {
   gsdRoot, milestonesDir, resolveMilestoneFile, resolveMilestonePath,
   resolveSliceFile, resolveSlicePath, resolveGsdRootFile, relGsdRootFile,
-  relMilestoneFile, relSliceFile,
+  relMilestoneFile, relSliceFile, clearPathCache,
 } from "./paths.js";
 import { join } from "node:path";
 import { readFileSync, existsSync, mkdirSync, readdirSync, rmSync, unlinkSync } from "node:fs";
 import { readSessionLockData, isSessionLockProcessAlive } from "./session-lock.js";
-import { nativeIsRepo, nativeInit } from "./native-git-bridge.js";
+import { nativeAddAll, nativeCommit, nativeHasCommittedHead, nativeIsRepo, nativeInit } from "./native-git-bridge.js";
 import { isInheritedRepo } from "./repo-identity.js";
 import { ensureGitignore, ensurePreferences, untrackRuntimeFiles } from "./gitignore.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
@@ -44,7 +52,9 @@ import { showProjectInit, offerMigration } from "./init-wizard.js";
 import { validateDirectory } from "./validate-directory.js";
 import { showConfirm } from "../shared/tui.js";
 import { debugLog } from "./debug-logger.js";
-import { findMilestoneIds, nextMilestoneId, reserveMilestoneId, getReservedMilestoneIds, clearReservedMilestoneIds } from "./milestone-ids.js";
+import { findMilestoneIds, clearReservedMilestoneIds } from "./milestone-ids.js";
+import { nextMilestoneIdReserved } from "./milestone-id-reservation.js";
+export { nextMilestoneIdReserved } from "./milestone-id-reservation.js";
 import { parkMilestone, discardMilestone } from "./milestone-actions.js";
 import { selectAndApplyModel } from "./auto-model-selection.js";
 import { DISCUSS_TOOLS_ALLOWLIST } from "./constants.js";
@@ -58,6 +68,8 @@ import {
   formatCodebaseBrief,
   formatPriorContextBrief,
 } from "./preparation.js";
+import { verifyExpectedArtifact } from "./auto-recovery.js";
+import { createWorkspace, scopeMilestone, type MilestoneScope } from "./workspace.js";
 
 // ─── Re-exports (preserve public API for existing importers) ────────────────
 export {
@@ -71,19 +83,47 @@ export {
   buildExistingMilestonesContext,
 } from "./guided-flow-queue.js";
 import { logWarning } from "./workflow-logger.js";
+import { deleteRuntimeKv } from "./db/runtime-kv.js";
+import { PAUSED_SESSION_KV_KEY } from "./interrupted-session.js";
+
+// ─── Scope-based validator wrappers ──────────────────────────────────────────
+// These thin wrappers accept a MilestoneScope so callers that already hold a
+// pinned scope never have to re-derive (basePath, milestoneId) separately.
+// The underlying implementations in auto-recovery.ts / auto-artifact-paths.ts /
+// state.ts are unchanged — only the call surface in guided-flow.ts is migrated.
 
-// ─── ID Generation with Reservation ─────────────────────────────────────────
+/**
+ * Scope-based overload of verifyExpectedArtifact.
+ * Uses scope.workspace.projectRoot as the authoritative base path, making
+ * the check immune to cwd-drift and worktree-path divergence.
+ */
+export function verifyExpectedArtifactForScope(
+  scope: MilestoneScope,
+  unitType: string,
+  unitId: string,
+): boolean {
+  return verifyExpectedArtifact(unitType, unitId, scope.workspace.projectRoot);
+}
 
 /**
- * Generate the next milestone ID, accounting for reserved IDs, and reserve it.
- * Ensures any preview ID shown in the UI matches what `gsd_milestone_generate_id`
- * will later return.
+ * Scope-based overload of resolveExpectedArtifactPath.
+ * Returns the canonical absolute path (or null) using the scope's projectRoot.
  */
-function nextMilestoneIdReserved(existingIds: string[], uniqueEnabled: boolean): string {
-  const allIds = [...new Set([...existingIds, ...getReservedMilestoneIds()])];
-  const id = nextMilestoneId(allIds, uniqueEnabled);
-  reserveMilestoneId(id);
-  return id;
+export function resolveExpectedArtifactPathForScope(
+  scope: MilestoneScope,
+  unitType: string,
+  unitId: string,
+): string | null {
+  return resolveExpectedArtifactPath(unitType, unitId, scope.workspace.projectRoot);
+}
+
+/**
+ * Scope-based overload of isGhostMilestone.
+ * Binds basePath and milestoneId from the scope, ensuring path resolution
+ * uses the canonical project root regardless of the cwd at call time.
+ */
+export function isGhostMilestoneByScope(scope: MilestoneScope): boolean {
+  return isGhostMilestone(scope.workspace.projectRoot, scope.milestoneId);
 }
 
 function needsPlanV2Gate(state: GSDState): boolean {
@@ -100,7 +140,7 @@ function runPlanV2Gate(
   basePath: string,
   state: GSDState,
 ): PlanV2GateDecision {
-  const prefs = loadEffectiveGSDPreferences()?.preferences;
+  const prefs = loadEffectiveGSDPreferences(basePath)?.preferences;
   const uokFlags = resolveUokFlags(prefs);
   if (!uokFlags.planV2 || !needsPlanV2Gate(state)) return "pass";
   const compiled = ensurePlanV2Graph(basePath, state);
@@ -138,36 +178,119 @@ interface PendingAutoStartEntry {
   // #4573: counter for how many times the LLM emitted the ready phrase
   // without writing the required artifacts. Cleared on entry delete/recreate.
   readyRejectCount?: number;
+  // C1: scope is pinned at reservation time so path resolution is immune to
+  // cwd-drift between discuss and checkAutoStartAfterDiscuss.
+  // TODO(C3): basePath becomes redundant once all consumers migrate to scope.
+  scope: MilestoneScope;
+  // H1: retry counter for Gate 1b plan-blocked recovery. Capped at
+  // MAX_PLAN_BLOCKED_RECOVERIES to prevent infinite recovery loops (#5012).
+  planBlockedRecoveryCount: number;
+}
+
+interface PendingDeepProjectSetupEntry {
+  ctx: ExtensionCommandContext;
+  pi: ExtensionAPI;
+  basePath: string;
+  step?: boolean;
+  createdAt: number;
+  sessionId?: string;
+  currentUnitType?: string;
+  currentUnitId?: string;
 }
 
 // #4573: cap for how many times we nudge the LLM after a premature ready
 // phrase before giving up and asking the user to re-run /gsd.
 const MAX_READY_REJECTS = 2;
 
+// H1 (#5012): cap for Gate 1b plan-blocked recovery hints. After this many
+// consecutive recovery attempts the loop is stopped and the user is directed
+// to investigate manually.
+const MAX_PLAN_BLOCKED_RECOVERIES = 3;
+
 // #4573: matches the canonical ready phrase the discuss prompt asks the LLM
 // to emit. Accepts any M-prefixed milestone ID (three digits + optional
 // suffix) with optional trailing punctuation.
 const READY_PHRASE_RE = /\bMilestone\s+M\d{3}[A-Z0-9-]*\s+ready\.?/i;
 
 const pendingAutoStartMap = new Map<string, PendingAutoStartEntry>();
+const pendingDeepProjectSetupMap = new Map<string, PendingDeepProjectSetupEntry>();
+const USER_DRIVEN_DEEP_SETUP_UNITS = new Set([
+  "discuss-project",
+  "discuss-requirements",
+  "research-decision",
+]);
+const FOREGROUND_DEEP_SETUP_RULE_NAMES = new Set([
+  "deep: pre-planning (no workflow prefs) → workflow-preferences",
+  "deep: pre-planning (no PROJECT) → discuss-project",
+  "deep: pre-planning (no REQUIREMENTS) → discuss-requirements",
+  "deep: pre-planning (no research decision) → research-decision",
+]);
+const LEGACY_DEEP_SETUP_PSEUDO_MILESTONE_DIRS = new Set([
+  "PROJECT",
+  "REQUIREMENTS",
+  "RESEARCH-DECISION",
+  "RESEARCH-PROJECT",
+  "WORKFLOW-PREFS",
+]);
+const FOREGROUND_DEEP_SETUP_QUESTION_POLICY = `## Foreground Deep Setup Question Policy
+
+This stage is running inside the foreground \`/gsd new-project --deep\` interview. Ask user questions in plain chat only.
+
+- Do NOT call \`ask_user_questions\`, \`AskUserQuestion\`, or ToolSearch to discover user-input tools.
+- Ask one focused round, then stop and wait for the user's normal chat response.`;
 
 /**
  * Backward-compat bridge: returns a mutable reference to the entry matching
  * basePath, or the sole entry when only one session exists.
- * Internal use only — external code should use the Map directly.
+ * Exported for testing — internal use only in production code.
  */
-function _getPendingAutoStart(basePath?: string): PendingAutoStartEntry | null {
+export function _getPendingAutoStart(basePath?: string): PendingAutoStartEntry | null {
   if (basePath) return pendingAutoStartMap.get(basePath) ?? null;
   if (pendingAutoStartMap.size === 1) return pendingAutoStartMap.values().next().value!;
   return null;
 }
 
+function hasNestedFileOrSymlink(dir: string): boolean {
+  for (const entry of readdirSync(dir, { withFileTypes: true })) {
+    if (entry.isFile() || entry.isSymbolicLink()) return true;
+    if (entry.isDirectory() && hasNestedFileOrSymlink(join(dir, entry.name))) return true;
+  }
+  return false;
+}
+
+function clearEmptyLegacyDeepSetupPseudoMilestones(basePath: string, entries: string[]): string[] {
+  const mDir = milestonesDir(basePath);
+  const remaining: string[] = [];
+  for (const entry of entries) {
+    if (!LEGACY_DEEP_SETUP_PSEUDO_MILESTONE_DIRS.has(entry)) {
+      remaining.push(entry);
+      continue;
+    }
+
+    const entryPath = join(mDir, entry);
+    try {
+      if (hasNestedFileOrSymlink(entryPath)) {
+        remaining.push(entry);
+        continue;
+      }
+      rmSync(entryPath, { recursive: true, force: true });
+      logWarning("guided", `Self-heal: removed empty legacy deep setup pseudo-milestone directory ${entry}`);
+    } catch (err) {
+      remaining.push(entry);
+      logWarning("guided", `legacy deep setup pseudo-milestone cleanup failed for ${entry}: ${(err as Error).message}`);
+    }
+  }
+  return remaining;
+}
+
 /**
  * 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; createdAt?: number }): void {
-  pendingAutoStartMap.set(basePath, { createdAt: Date.now(), ...entry } as PendingAutoStartEntry);
+  const ws = createWorkspace(entry.basePath);
+  const scope = scopeMilestone(ws, entry.milestoneId);
+  pendingAutoStartMap.set(basePath, { createdAt: Date.now(), planBlockedRecoveryCount: 0, ...entry, scope } as PendingAutoStartEntry);
 }
 
 /**
@@ -183,6 +306,14 @@ export function clearPendingAutoStart(basePath?: string): void {
   }
 }
 
+export function clearPendingDeepProjectSetup(basePath?: string): void {
+  if (basePath) {
+    pendingDeepProjectSetupMap.delete(basePath);
+  } else {
+    pendingDeepProjectSetupMap.clear();
+  }
+}
+
 /**
  * Returns the milestoneId being discussed for the given project.
  * When basePath is omitted and only one session is active, returns that
@@ -200,6 +331,153 @@ export function getDiscussionMilestoneId(basePath?: string): string | null {
   return null;
 }
 
+function _getPendingDeepProjectSetup(basePath?: string): PendingDeepProjectSetupEntry | null {
+  if (basePath) return pendingDeepProjectSetupMap.get(basePath) ?? null;
+  if (pendingDeepProjectSetupMap.size === 1) return pendingDeepProjectSetupMap.values().next().value!;
+  return null;
+}
+
+function getDeepSetupSessionId(ctx: ExtensionContext | undefined): string | undefined {
+  return ctx?.sessionManager?.getSessionId?.();
+}
+
+function _getPendingDeepProjectSetupForContext(
+  ctx: ExtensionContext | undefined,
+  basePath?: string,
+): PendingDeepProjectSetupEntry | null {
+  if (basePath) {
+    const direct = pendingDeepProjectSetupMap.get(basePath);
+    if (direct) return direct;
+  }
+  if (!ctx) return _getPendingDeepProjectSetup();
+
+  const sessionId = getDeepSetupSessionId(ctx);
+  if (sessionId) {
+    const matches = [...pendingDeepProjectSetupMap.values()].filter(entry => entry.sessionId === sessionId);
+    if (matches.length === 1) return matches[0]!;
+  }
+
+  const matches = [...pendingDeepProjectSetupMap.values()].filter(entry => entry.ctx === ctx);
+  return matches.length === 1 ? matches[0]! : null;
+}
+
+export function getPendingDeepProjectSetupUnitForContext(
+  ctx: ExtensionContext | undefined,
+  basePath?: string,
+): { unitType: string; unitId: string } | null {
+  const entry = _getPendingDeepProjectSetupForContext(ctx, basePath);
+  if (!entry?.currentUnitType || !entry.currentUnitId) return null;
+  return {
+    unitType: entry.currentUnitType,
+    unitId: entry.currentUnitId,
+  };
+}
+
+export async function startDeepProjectSetupForeground(
+  ctx: ExtensionCommandContext,
+  pi: ExtensionAPI,
+  basePath: string,
+  step?: boolean,
+): Promise<void> {
+  const entry: PendingDeepProjectSetupEntry = {
+    ctx,
+    pi,
+    basePath,
+    step,
+    createdAt: Date.now(),
+    sessionId: getDeepSetupSessionId(ctx),
+  };
+  pendingDeepProjectSetupMap.set(basePath, entry);
+  await dispatchNextDeepProjectSetupStage(entry);
+}
+
+export async function checkDeepProjectSetupAfterTurn(
+  _event: { messages: any[] },
+  ctx?: ExtensionContext,
+  basePath?: string,
+): Promise<boolean> {
+  const entry = _getPendingDeepProjectSetupForContext(ctx, basePath);
+  if (!entry) return false;
+
+  if (entry.currentUnitType && entry.currentUnitId) {
+    // TODO(C-future): PendingDeepProjectSetupEntry does not carry a MilestoneScope
+    // because deep-project-setup units span non-milestone unit types (discuss-project,
+    // discuss-requirements, etc.).  Migrate to verifyExpectedArtifactForScope once
+    // PendingDeepProjectSetupEntry is extended with a scope field.
+    const artifactReady = verifyExpectedArtifact(entry.currentUnitType, entry.currentUnitId, entry.basePath);
+    if (!artifactReady) {
+      return false;
+    }
+  }
+
+  return dispatchNextDeepProjectSetupStage(entry);
+}
+
+async function dispatchNextDeepProjectSetupStage(entry: PendingDeepProjectSetupEntry): Promise<boolean> {
+  invalidateAllCaches();
+  const prefs = loadEffectiveGSDPreferences(entry.basePath)?.preferences;
+  const { DISPATCH_RULES, hasPendingDeepStage } = await import("./auto-dispatch.js");
+
+  if (!hasPendingDeepStage(prefs, entry.basePath)) {
+    pendingDeepProjectSetupMap.delete(entry.basePath);
+    startAutoDetached(entry.ctx, entry.pi, entry.basePath, false, { step: entry.step });
+    return true;
+  }
+
+  const state = await deriveState(entry.basePath);
+  const dispatchCtx = {
+    basePath: entry.basePath,
+    mid: "PROJECT",
+    midTitle: "Project setup",
+    state,
+    prefs,
+    // Claude Code currently surfaces workflow-MCP question calls as tool-request
+    // UI that can be cancelled outside the normal chat flow. During the
+    // foreground deep project setup interview, keep user input in plain chat so
+    // `/gsd new-project --deep` cannot bounce through cancelled tool requests.
+    structuredQuestionsAvailable: "false" as const,
+  };
+  let result: Awaited<ReturnType<(typeof DISPATCH_RULES)[number]["match"]>> = null;
+  for (const rule of DISPATCH_RULES) {
+    // Only evaluate foreground setup gates here. Later deep rules such as
+    // research-project have dispatch-time side effects (e.g. claiming an
+    // inflight marker) and must be left to auto-mode once the interview is
+    // complete.
+    if (!FOREGROUND_DEEP_SETUP_RULE_NAMES.has(rule.name)) continue;
+    result = await rule.match(dispatchCtx);
+    if (result) break;
+  }
+
+  if (!result || result.action !== "dispatch") {
+    if (result?.action === "stop") {
+      entry.ctx.ui.notify(result.reason, result.level);
+    } else if (hasPendingDeepStage(prefs, entry.basePath)) {
+      pendingDeepProjectSetupMap.delete(entry.basePath);
+      startAutoDetached(entry.ctx, entry.pi, entry.basePath, false, { step: entry.step });
+      return true;
+    }
+    return false;
+  }
+
+  if (!USER_DRIVEN_DEEP_SETUP_UNITS.has(result.unitType)) {
+    pendingDeepProjectSetupMap.delete(entry.basePath);
+    startAutoDetached(entry.ctx, entry.pi, entry.basePath, false, { step: entry.step });
+    return true;
+  }
+
+  entry.currentUnitType = result.unitType;
+  entry.currentUnitId = result.unitId;
+  entry.createdAt = Date.now();
+  await dispatchWorkflow(
+    entry.pi,
+    `${result.prompt}\n\n${FOREGROUND_DEEP_SETUP_QUESTION_POLICY}`,
+    "gsd-run",
+    entry.ctx,
+    result.unitType,
+  );
+  return true;
+}
+
 /** Called from agent_end to check if auto-mode should start after discuss */
 export function checkAutoStartAfterDiscuss(): boolean {
   const entry = _getPendingAutoStart();
@@ -209,17 +487,77 @@ export function checkAutoStartAfterDiscuss(): boolean {
 
   // Gate 1: Primary milestone must have CONTEXT.md or ROADMAP.md
   // The "discuss" path creates CONTEXT.md; the "plan" path creates ROADMAP.md.
-  const contextFile = resolveMilestoneFile(basePath, milestoneId, "CONTEXT");
-  const roadmapFile = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
+  // Use pinned scope (immune to cwd-drift) for existence checks.
+  const contextFilePath = entry.scope.contextFile();
+  const roadmapFilePath = entry.scope.roadmapFile();
+  const contextFile = existsSync(contextFilePath) ? contextFilePath : null;
+  const roadmapFile = existsSync(roadmapFilePath) ? roadmapFilePath : null;
   if (!contextFile && !roadmapFile) return false; // neither artifact yet — keep waiting
 
+  // Gate 1b: Discriminate plan-blocked from discuss-incomplete when the DB row is queued.
+  // If the DB is available and the row is still "queued" but CONTEXT.md already exists on
+  // disk, the discuss phase completed but gsd_plan_milestone was hard-blocked by the
+  // depth-verification gate.  Emit a recovery hint so the next agent turn can retry
+  // gsd_plan_milestone, then return false (keep blocking auto-start).
+  // If CONTEXT.md does not exist (discuss-incomplete), Gate 1 already blocked above.
+  if (isDbAvailable()) {
+    const dbRow = getMilestone(milestoneId);
+    if (dbRow?.status === "queued" && contextFile) {
+      if (entry.planBlockedRecoveryCount >= MAX_PLAN_BLOCKED_RECOVERIES) {
+        // H1: recovery loop cap reached — stop triggering new turns, escalate to user.
+        logWarning(
+          "guided",
+          `Gate 1b: milestone ${milestoneId} plan-blocked recovery limit reached ` +
+          `(${entry.planBlockedRecoveryCount}/${MAX_PLAN_BLOCKED_RECOVERIES}); escalating to user`,
+        );
+        ctx.ui.notify(
+          `Milestone ${milestoneId} plan_milestone has been blocked ${entry.planBlockedRecoveryCount} times. ` +
+          `Re-run /gsd to reset the recovery counter, or run /gsd-debug to diagnose without resetting.`,
+          "error",
+        );
+        return false;
+      }
+      logWarning(
+        "guided",
+        `Gate 1b: milestone ${milestoneId} queued with CONTEXT.md present — ` +
+        `plan_milestone was blocked; emitting recovery hint ` +
+        `(attempt ${entry.planBlockedRecoveryCount + 1}/${MAX_PLAN_BLOCKED_RECOVERIES})`,
+      );
+      ctx.ui.notify(
+        `Milestone ${milestoneId}: context file exists but milestone is still queued. ` +
+        `Retrying gsd_plan_milestone to complete the blocked planning step.`,
+        "warning",
+      );
+      try {
+        pi.sendMessage(
+          {
+            customType: "gsd-plan-milestone-blocked-recovery",
+            content:
+              `Milestone ${milestoneId} has ${contextFile} on disk but its DB row is still ` +
+              `"queued". The gsd_plan_milestone tool was previously blocked by the ` +
+              `depth-verification gate. Call gsd_plan_milestone now to complete the ` +
+              `planning phase.`,
+            display: false,
+          },
+          { triggerTurn: true },
+        );
+        // Increment only after a successful dispatch so transient sendMessage
+        // failures do not consume recovery budget.
+        entry.planBlockedRecoveryCount += 1;
+      } catch (e) {
+        logWarning("guided", `Gate 1b recovery sendMessage failed: ${(e as Error).message}`);
+      }
+      return false;
+    }
+  }
+
   // 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
+  const stateFilePath = entry.scope.stateFile();
+  if (!existsSync(stateFilePath)) return false; // discussion not finalized yet
 
   // Gate 3: Multi-milestone completeness warning
   // Parse PROJECT.md for milestone sequence, warn if any are missing context.
@@ -252,7 +590,7 @@ export function checkAutoStartAfterDiscuss(): boolean {
   // The LLM writes DISCUSSION-MANIFEST.json after each Phase 3 gate decision.
   // When it exists, validate it before auto-starting. Project history alone is
   // not a reliable signal for the current discussion mode.
-  const manifestPath = join(gsdRoot(basePath), "DISCUSSION-MANIFEST.json");
+  const manifestPath = join(entry.scope.workspace.contract.projectGsd, "DISCUSSION-MANIFEST.json");
   if (existsSync(manifestPath)) {
     try {
       const manifest = JSON.parse(readFileSync(manifestPath, "utf-8"));
@@ -343,13 +681,15 @@ function hasToolUse(msg: any): boolean {
 /**
  * #4573 — Detect and recover from the "ready phrase without files" failure mode.
  *
- * When the LLM emits "Milestone {{id}} ready." but has not written CONTEXT.md
- * or ROADMAP.md, `checkAutoStartAfterDiscuss()` silently returns false and the
- * next /gsd invocation loops into the "All milestones complete" warning.
+ * When the LLM emits "Milestone {{id}} ready." but has not written the
+ * milestone CONTEXT/ROADMAP artifacts, `checkAutoStartAfterDiscuss()` silently
+ * returns false and the next /gsd invocation loops into the "All milestones
+ * complete" warning.
  *
  * This function, called from `handleAgentEnd` after `checkAutoStartAfterDiscuss`
  * returns false, pattern-matches the ready phrase on the last assistant message.
- * If it fired AND neither CONTEXT.md nor ROADMAP.md exists, it:
+ * If it fired AND neither the canonical M###-CONTEXT.md/M###-ROADMAP.md nor
+ * legacy CONTEXT.md/ROADMAP.md files exist, it:
  *   1. Notifies the user that the signal was rejected.
  *   2. Injects a system message via `pi.sendMessage(..., {triggerTurn:true})`
  *      telling the LLM the signal was premature and to emit the writes now.
@@ -369,12 +709,39 @@ export function maybeHandleReadyPhraseWithoutFiles(event: { messages: any[] }):
   const text = extractAssistantText(lastMsg);
   if (!READY_PHRASE_RE.test(text)) return false;
 
+  // Bust paths.ts cached dir listings before checking for fresh writes. The
+  // LLM's Write tool calls do not invalidate paths.ts caches, so a stale
+  // listing taken before the milestone dir or its CONTEXT/ROADMAP files
+  // existed would falsely report the artifacts as missing and trigger the
+  // 3-strike "ready without files" abort even though the writes succeeded.
+  clearPathCache();
+
   // Gate: artifacts must still be missing — if they exist, the happy path
   // already fired and we have nothing to do.
   const contextFile = resolveMilestoneFile(basePath, milestoneId, "CONTEXT");
   const roadmapFile = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
   if (contextFile || roadmapFile) return false;
 
+  // Diagnostic: when the cached resolver reports both files missing, also probe
+  // the canonical paths with uncached existsSync so we can tell whether the
+  // recovery is firing on real-missing files or a path-resolution miss
+  // (basePath/symlink mismatch, stale cache despite agent-end-recovery flush,
+  // legacy descriptor dir not matching, etc.).
+  try {
+    const mDir = resolveMilestonePath(basePath, milestoneId);
+    const canonicalCtx = mDir ? join(mDir, `${milestoneId}-CONTEXT.md`) : null;
+    const canonicalRoadmap = mDir ? join(mDir, `${milestoneId}-ROADMAP.md`) : null;
+    logWarning(
+      "guided",
+      `ready-phrase-reject diagnostic mid=${milestoneId} basePath=${basePath} ` +
+      `mDir=${mDir ?? "null"} ` +
+      `canonical-ctx=${canonicalCtx ?? "null"} ctx-exists=${canonicalCtx ? existsSync(canonicalCtx) : "n/a"} ` +
+      `canonical-roadmap=${canonicalRoadmap ?? "null"} roadmap-exists=${canonicalRoadmap ? existsSync(canonicalRoadmap) : "n/a"}`,
+    );
+  } catch (e) {
+    logWarning("guided", `ready-phrase-reject diagnostic failed: ${(e as Error).message}`);
+  }
+
   entry.readyRejectCount = (entry.readyRejectCount ?? 0) + 1;
 
   if (entry.readyRejectCount > MAX_READY_REJECTS) {
@@ -389,15 +756,16 @@ export function maybeHandleReadyPhraseWithoutFiles(event: { messages: any[] }):
     return true;
   }
 
+  const contextRel = relMilestoneFile(basePath, milestoneId, "CONTEXT");
+  const roadmapRel = relMilestoneFile(basePath, milestoneId, "ROADMAP");
   ctx.ui.notify(
-    `Milestone ${milestoneId}: "ready" signal rejected — CONTEXT.md and ROADMAP.md are missing. Asking the LLM to complete the writes.`,
+    `Milestone ${milestoneId}: "ready" signal rejected — ${contextRel} and ${roadmapRel} are missing. Asking the LLM to complete the writes.`,
     "warning",
   );
 
   const nudge =
     `You emitted "Milestone ${milestoneId} ready." but neither ` +
-    `.gsd/milestones/${milestoneId}/${milestoneId}-CONTEXT.md nor ` +
-    `.gsd/milestones/${milestoneId}/${milestoneId}-ROADMAP.md exists on disk. ` +
+    `${contextRel} nor ${roadmapRel} exists on disk. ` +
     `The ready phrase is a POST-WRITE signal and has been rejected. ` +
     `In this turn: (1) write PROJECT.md, REQUIREMENTS.md, and the milestone ` +
     `CONTEXT.md, (2) call gsd_plan_milestone, then (3) emit the ready phrase. ` +
@@ -440,8 +808,13 @@ const MAX_EMPTY_TURN_RETRIES = 2;
 
 // Phrases that indicate the LLM is about to do something but has not yet.
 // Kept tight to avoid flagging legitimate narration like "I'll wait for your answer."
+//
+// "make" was previously in the verb list but matches conversational meta phrases
+// like "Let me make sure I understand…" which are NOT action announcements —
+// removed to prevent the empty-turn nudge from auto-replying to user questions
+// in discuss flows.
 const COMMIT_INTENT_RE =
-  /\b(?:I['’]ll|I will|Next,? I['’]ll|Now I['’]ll|Let me|I['’]m going to|I am going to)\s+(?:now\s+)?(?:write|create|call|invoke|update|add|make|run|execute|generate|produce|emit|compose|implement|save|apply|commit)\b/i;
+  /\b(?:I['’]ll|I will|Next,? I['’]ll|Now I['’]ll|Let me|I['’]m going to|I am going to)\s+(?:now\s+)?(?:write|create|call|invoke|update|add|run|execute|generate|produce|emit|compose|implement|save|apply|commit)\b/i;
 
 /**
  * Reset the empty-turn counter for a basePath after a successful tool-use turn.
@@ -471,12 +844,14 @@ export function maybeHandleEmptyIntentTurn(
   // path, handled by maybeHandleReadyPhraseWithoutFiles.
   if (READY_PHRASE_RE.test(text)) return false;
 
-  // Skip if the LLM is clearly handing back to the user. Keep the heuristic
-  // tight: a trailing question mark on the last non-empty line is the common
-  // signal for "I asked the user a question and stopped."
-  const lines = text.split(/\r?\n/).map((l) => l.trim()).filter(Boolean);
-  const lastLine = lines[lines.length - 1] ?? "";
-  if (lastLine.endsWith("?")) return false;
+  // Skip if the LLM is clearly handing back to the user. Discuss flows
+  // often pose a question and follow it with a conditional intent on the
+  // same line ("Did I capture that correctly? If so, I'll write the
+  // requirements."). A line-trailing `?` check misses these because the
+  // line ends in `.`. Match any sentence-terminating `?` (followed by
+  // whitespace or end-of-text) — false negatives here auto-reply to the
+  // user, which is a much worse failure mode than a missed nudge.
+  if (/\?(?:\s|$)/.test(text)) return false;
 
   // Must contain a commit-intent phrase — this is the stall we care about.
   if (!COMMIT_INTENT_RE.test(text)) return false;
@@ -619,7 +994,7 @@ async function dispatchWorkflow(
     });
   }
 
-  const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(process.env.HOME ?? "~", ".gsd", "agent", "GSD-WORKFLOW.md");
+  const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(gsdHome(), "agent", "GSD-WORKFLOW.md");
   const workflow = readFileSync(workflowPath, "utf-8");
 
   pi.sendMessage(
@@ -832,20 +1207,25 @@ export async function showHeadlessMilestoneCreation(
   // Ensure .gsd/ is bootstrapped
   bootstrapGsdProject(basePath);
 
+  const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+  await ensureDbOpen(basePath);
+
   // Generate next milestone ID
   const existingIds = findMilestoneIds(basePath);
   const prefs = loadEffectiveGSDPreferences();
-  const nextId = nextMilestoneIdReserved(existingIds, prefs?.preferences?.unique_milestone_ids ?? false);
+  const nextId = nextMilestoneIdReserved(existingIds, prefs?.preferences?.unique_milestone_ids ?? false, basePath);
 
-  // Create milestone directory
-  const milestoneDir = join(gsdRoot(basePath), "milestones", nextId, "slices");
-  mkdirSync(milestoneDir, { recursive: true });
+  // Fix #4996: Do NOT pre-create the milestone directory here.
+  // atomicWriteAsync (used by all artifact writers) calls mkdir lazily before
+  // each write, so every path through saveArtifactToDb / saveFile is already
+  // lazy-mkdir-safe. Pre-creating the dir before the discuss flow runs leaves
+  // an orphan stub if discuss is abandoned — that stub later skews nextMilestoneId.
 
   // Build and dispatch the headless discuss prompt
   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, createdAt: Date.now() });
+  setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: nextId });
 
   // Dispatch as discuss-milestone. The LLM writes PROJECT.md, REQUIREMENTS.md,
   // and CONTEXT.md, then calls gsd_plan_milestone — this is semantically the
@@ -1042,22 +1422,24 @@ 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, createdAt: Date.now() });
+      setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: mid, step: false });
       await dispatchWorkflow(pi, seed, "gsd-discuss", ctx, "discuss-milestone");
     } else if (choice === "discuss_fresh") {
       const discussMilestoneTemplates = inlineTemplate("context", "Context");
       const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: mid, step: false, createdAt: Date.now() });
+      setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: mid, step: false });
       await dispatchWorkflow(pi, loadPrompt("guided-discuss-milestone", {
         milestoneId: mid, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
         commitInstruction: buildDocsCommitInstruction(`docs(${mid}): milestone context from discuss`),
         fastPathInstruction: "",
       }), "gsd-discuss", ctx, "discuss-milestone");
     } else if (choice === "skip_milestone") {
+      const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+      await ensureDbOpen(basePath);
       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, createdAt: Date.now() });
+      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
+      setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: nextId, step: false });
       await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId, `New milestone ${nextId}.`, basePath), "gsd-run", ctx, "discuss-milestone");
     }
     return;
@@ -1348,6 +1730,9 @@ function selfHealRuntimeRecords(basePath: string, ctx: ExtensionContext): { clea
     for (const record of records) {
       const { unitType, unitId, phase } = record;
       // Clear records whose expected artifact already exists (completed but not cleaned up)
+      // TODO(C-future): selfHealRuntimeRecords iterates across all unit types (not just milestone
+      // units), so it cannot be converted to resolveExpectedArtifactPathForScope without
+      // first establishing a per-record scope.  Migrate once unit runtime records carry scope info.
       const artifactPath = resolveExpectedArtifactPath(unitType, unitId, basePath);
       if (artifactPath && existsSync(artifactPath)) {
         clearUnitRuntimeRecord(basePath, unitType, unitId);
@@ -1461,8 +1846,8 @@ async function handleMilestoneActions(
   if (choice === "skip") {
     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, createdAt: Date.now() });
+    const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
+    setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
     await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
       `New milestone ${nextId}.`,
       basePath
@@ -1509,6 +1894,7 @@ export async function showSmartEntry(
   // milestones/) must trigger the init wizard, not skip it (#2942).
   const gsdPath = gsdRoot(basePath);
   const hasBootstrapArtifacts = hasGsdBootstrapArtifacts(gsdPath);
+  let skipGitBootstrap = false;
 
   if (!hasBootstrapArtifacts) {
     const detection = detectProjectState(basePath);
@@ -1528,6 +1914,7 @@ export async function showSmartEntry(
     // No .gsd/ or zombie .gsd/ — run the project init wizard
     const result = await showProjectInit(ctx, pi, basePath, detection);
     if (!result.completed) return; // User cancelled
+    skipGitBootstrap = result.gitEnabled === false;
 
     // Init wizard bootstrapped .gsd/ — fall through to the normal flow below
     // which will detect "no milestones" and start the discuss prompt
@@ -1537,14 +1924,34 @@ export async function showSmartEntry(
   // Also handle inherited repos: if basePath is a subdirectory of another
   // git repo that has no .gsd, create a fresh repo to prevent cross-project
   // state leaks (#1639).
-  if (!nativeIsRepo(basePath) || isInheritedRepo(basePath)) {
+  if (!skipGitBootstrap && (!nativeIsRepo(basePath) || isInheritedRepo(basePath))) {
     const mainBranch = loadEffectiveGSDPreferences()?.preferences?.git?.main_branch || "main";
     nativeInit(basePath, mainBranch);
   }
 
   // ── Ensure .gitignore has baseline patterns ──────────────────────────
-  ensureGitignore(basePath);
-  untrackRuntimeFiles(basePath);
+  if (!skipGitBootstrap && nativeIsRepo(basePath)) {
+    ensureGitignore(basePath);
+    untrackRuntimeFiles(basePath);
+  }
+
+  // Deep setup can pre-create .gsd/PREFERENCES.md before the normal init
+  // wizard path runs. If that path also initialized git, make HEAD reachable
+  // now so later worktree/git-log operations do not run on an unborn branch.
+  if (!skipGitBootstrap && nativeIsRepo(basePath) && !nativeHasCommittedHead(basePath)) {
+    try {
+      nativeAddAll(basePath);
+      nativeCommit(basePath, "chore: init project");
+    } catch (err) {
+      const message = err instanceof Error ? err.message : String(err);
+      logWarning("guided", `initial git commit failed; worktree isolation will remain disabled until HEAD exists: ${message}`);
+    }
+  }
+
+  {
+    const { ensureDbOpen } = await import("./bootstrap/dynamic-tools.js");
+    await ensureDbOpen(basePath);
+  }
 
   // ── Self-heal stale runtime records from crashed auto-mode sessions ──
   selfHealRuntimeRecords(basePath, ctx);
@@ -1558,10 +1965,12 @@ export async function showSmartEntry(
   if (interrupted.classification === "stale") {
     clearLock(basePath);
     if (interrupted.pausedSession) {
+      // Phase C pt 2: paused-session.json migrated to runtime_kv
+      // (global scope, key PAUSED_SESSION_KV_KEY).
       try {
-        unlinkSync(join(gsdRoot(basePath), "runtime", "paused-session.json"));
+        deleteRuntimeKv("global", "", PAUSED_SESSION_KV_KEY);
       } catch (e) {
-        logWarning("guided", `stale pause file cleanup failed: ${(e as Error).message}`, { file: "guided-flow.ts" });
+        logWarning("guided", `stale paused-session DB cleanup failed: ${(e as Error).message}`, { file: "guided-flow.ts" });
       }
     }
   } else if (interrupted.classification === "recoverable") {
@@ -1598,6 +2007,23 @@ export async function showSmartEntry(
     logWarning("guided", `STATE.md rebuild failed: ${(err as Error).message}`);
   }
 
+  // ── Deep planning mode kickoff ────────────────────────────────────────
+  // When `planning_depth: deep` is set (e.g. via `/gsd new-project --deep`)
+  // and any project-level stage gate is still pending, keep the user-question
+  // stages in the foreground conversation. Auto-mode is resumed only after
+  // the project interview artifacts exist, so questions do not look like
+  // cancelled auto-mode runs.
+  // Light mode and fully-completed deep projects fall through to the
+  // standard wizard below.
+  {
+    const prefs = loadEffectiveGSDPreferences(basePath)?.preferences;
+    const { hasPendingDeepStage } = await import("./auto-dispatch.js");
+    if (hasPendingDeepStage(prefs, basePath)) {
+      await startDeepProjectSetupForeground(ctx, pi, basePath, stepMode);
+      return;
+    }
+  }
+
   const planV2GateDecision = runPlanV2Gate(ctx, basePath, state);
   if (planV2GateDecision === "block") return;
 
@@ -1608,14 +2034,12 @@ 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 staleness: no manifest, no CONTEXT.md, AND entry is older than
+      // Detect staleness: no manifest, no milestone CONTEXT artifact, 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`),
-      );
+      const milestoneHasContext = !!resolveMilestoneFile(basePath, entry.milestoneId, "CONTEXT");
       if (!manifestExists && !milestoneHasContext && ageMs > 30_000) {
         // Stale entry from an interrupted discussion — clear and continue
         pendingAutoStartMap.delete(basePath);
@@ -1634,7 +2058,7 @@ export async function showSmartEntry(
       const mDir = milestonesDir(basePath);
       if (existsSync(mDir)) {
         try {
-          const entries = readdirSync(mDir);
+          const entries = clearEmptyLegacyDeepSetupPseudoMilestones(basePath, readdirSync(mDir));
           if (entries.length > 0) {
             ctx.ui.notify(
               `Milestone directory has ${entries.length} entries but none were recognized as milestones. ` +
@@ -1648,12 +2072,12 @@ export async function showSmartEntry(
     }
 
     const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-    const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+    const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
     const isFirst = milestoneIds.length === 0;
 
     if (isFirst) {
       // First ever — skip wizard, just ask directly
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
+      setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
       await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
         `New project, milestone ${nextId}. Do NOT read or explore .gsd/ — it's empty scaffolding.`,
         basePath
@@ -1674,7 +2098,7 @@ export async function showSmartEntry(
       });
 
       if (choice === "new_milestone") {
-        pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
+        setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
         await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
           `New milestone ${nextId}.`,
           basePath
@@ -1688,7 +2112,7 @@ export async function showSmartEntry(
   const milestoneTitle = state.activeMilestone.title;
 
   if (planV2GateDecision === "recover-missing-context") {
-    pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode, createdAt: Date.now() });
+    setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId, step: stepMode });
     await dispatchWorkflow(
       pi,
       await buildDiscussMilestonePrompt(
@@ -1728,9 +2152,9 @@ export async function showSmartEntry(
     if (choice === "new_milestone") {
       const milestoneIds = findMilestoneIds(basePath);
       const uniqueMilestoneIds = !!loadEffectiveGSDPreferences()?.preferences?.unique_milestone_ids;
-      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds);
+      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
 
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode, createdAt: Date.now() });
+      setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
       await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
         `New milestone ${nextId}.`,
         basePath
@@ -1782,12 +2206,12 @@ export async function showSmartEntry(
       const seed = draftContent
         ? `${basePrompt}\n\n## Prior Discussion (Draft Seed)\n\n${draftContent}`
         : basePrompt;
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode, createdAt: Date.now() });
+      setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId, step: stepMode });
       await dispatchWorkflow(pi, seed, "gsd-discuss", ctx, "discuss-milestone");
     } else if (choice === "discuss_fresh") {
       const discussMilestoneTemplates = inlineTemplate("context", "Context");
       const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
-      pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode, createdAt: Date.now() });
+      setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId, step: stepMode });
       await dispatchWorkflow(pi, loadPrompt("guided-discuss-milestone", {
         milestoneId, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
         commitInstruction: buildDocsCommitInstruction(`docs(${milestoneId}): milestone context from discuss`),
@@ -1796,8 +2220,8 @@ export async function showSmartEntry(
     } else if (choice === "skip_milestone") {
       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, createdAt: Date.now() });
+      const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
+      setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
       await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
         `New milestone ${nextId}.`,
         basePath
@@ -1862,26 +2286,14 @@ export async function showSmartEntry(
       });
 
       if (choice === "plan") {
-        pendingAutoStartMap.set(basePath, { ctx, pi, basePath, milestoneId, step: stepMode, createdAt: Date.now() });
-        const planMilestoneTemplates = [
-          inlineTemplate("roadmap", "Roadmap"),
-          inlineTemplate("plan", "Slice Plan"),
-          inlineTemplate("task-plan", "Task Plan"),
-          inlineTemplate("secrets-manifest", "Secrets Manifest"),
-        ].join("\n\n---\n\n");
-        const secretsOutputPath = relMilestoneFile(basePath, milestoneId, "SECRETS");
-        await dispatchWorkflow(pi, loadPrompt("guided-plan-milestone", {
-          milestoneId,
-          milestoneTitle,
-          secretsOutputPath,
-          inlinedTemplates: planMilestoneTemplates,
-          skillActivation: buildSkillActivationBlock({
-            base: basePath,
-            milestoneId,
-            milestoneTitle,
-            extraContext: [planMilestoneTemplates],
-          }),
-        }), "gsd-run", ctx, "plan-milestone");
+        setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId, step: stepMode });
+        await dispatchWorkflow(
+          pi,
+          await buildPlanMilestonePrompt(milestoneId, milestoneTitle, basePath),
+          "gsd-run",
+          ctx,
+          "plan-milestone",
+        );
       } else if (choice === "discuss") {
         const discussMilestoneTemplates = inlineTemplate("context", "Context");
         const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
@@ -1893,8 +2305,8 @@ export async function showSmartEntry(
       } else if (choice === "skip_milestone") {
         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, createdAt: Date.now() });
+        const nextId = nextMilestoneIdReserved(milestoneIds, uniqueMilestoneIds, basePath);
+        setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: nextId, step: stepMode });
         await dispatchWorkflow(pi, await prepareAndBuildDiscussPrompt(ctx, pi, nextId,
           `New milestone ${nextId}.`,
           basePath
@@ -2006,23 +2418,13 @@ export async function showSmartEntry(
     });
 
     if (choice === "plan") {
-      const planSliceTemplates = [
-        inlineTemplate("plan", "Slice Plan"),
-        inlineTemplate("task-plan", "Task Plan"),
-      ].join("\n\n---\n\n");
-      await dispatchWorkflow(pi, loadPrompt("guided-plan-slice", {
-        milestoneId,
-        sliceId,
-        sliceTitle,
-        inlinedTemplates: planSliceTemplates,
-        skillActivation: buildSkillActivationBlock({
-          base: basePath,
-          milestoneId,
-          sliceId,
-          sliceTitle,
-          extraContext: [planSliceTemplates],
-        }),
-      }), "gsd-run", ctx, "plan-slice");
+      await dispatchWorkflow(
+        pi,
+        await buildPlanSlicePrompt(milestoneId, milestoneTitle, sliceId, sliceTitle, basePath),
+        "gsd-run",
+        ctx,
+        "plan-slice",
+      );
     } else if (choice === "discuss") {
       const sqAvail = getStructuredQuestionsAvailability(pi, ctx);
       await dispatchWorkflow(pi, await buildDiscussSlicePrompt(milestoneId, sliceId, sliceTitle, basePath, { rediscuss: hasContext, structuredQuestionsAvailable: sqAvail }), "gsd-run", ctx, "discuss-slice");
@@ -2078,24 +2480,13 @@ export async function showSmartEntry(
     });
 
     if (choice === "complete") {
-      const completeSliceTemplates = [
-        inlineTemplate("slice-summary", "Slice Summary"),
-        inlineTemplate("uat", "UAT"),
-      ].join("\n\n---\n\n");
-      await dispatchWorkflow(pi, loadPrompt("guided-complete-slice", {
-        workingDirectory: basePath,
-        milestoneId,
-        sliceId,
-        sliceTitle,
-        inlinedTemplates: completeSliceTemplates,
-        skillActivation: buildSkillActivationBlock({
-          base: basePath,
-          milestoneId,
-          sliceId,
-          sliceTitle,
-          extraContext: [completeSliceTemplates],
-        }),
-      }), "gsd-run", ctx, "complete-slice");
+      await dispatchWorkflow(
+        pi,
+        await buildCompleteSlicePrompt(milestoneId, milestoneTitle, sliceId, sliceTitle, basePath),
+        "gsd-run",
+        ctx,
+        "complete-slice",
+      );
     } else if (choice === "status") {
       const { fireStatusViaCommand } = await import("./commands.js");
       await fireStatusViaCommand(ctx);
@@ -2170,22 +2561,13 @@ export async function showSmartEntry(
           }),
         }), "gsd-run", ctx, "execute-task");
       } else {
-        const executeTaskTemplates = inlineTemplate("task-summary", "Task Summary");
-        await dispatchWorkflow(pi, loadPrompt("guided-execute-task", {
-          milestoneId,
-          sliceId,
-          taskId,
-          taskTitle,
-          inlinedTemplates: executeTaskTemplates,
-          skillActivation: buildSkillActivationBlock({
-            base: basePath,
-            milestoneId,
-            sliceId,
-            taskId,
-            taskTitle,
-            extraContext: [executeTaskTemplates],
-          }),
-        }), "gsd-run", ctx, "execute-task");
+        await dispatchWorkflow(
+          pi,
+          await buildExecuteTaskPrompt(milestoneId, sliceId, sliceTitle, taskId, taskTitle, basePath),
+          "gsd-run",
+          ctx,
+          "execute-task",
+        );
       }
     } else if (choice === "status") {
       const { fireStatusViaCommand } = await import("./commands.js");