gsd-pi 2.76.0-dev.4100bd590 → 2.76.0-dev.479ad0e78

package/src/resources/extensions/gsd/auto-worktree.ts

@@ -238,14 +238,6 @@ function clearProjectRootStateFiles(basePath: string, milestoneId: string): void
   }
 }
 
-function isProjectGsdSymlink(basePath: string): boolean {
-  try {
-    return lstatSyncFn(join(basePath, ".gsd")).isSymbolicLink();
-  } catch {
-    return false;
-  }
-}
-
 // ─── Build Artifact Auto-Resolve ─────────────────────────────────────────────
 
 /** Patterns for machine-generated build artifacts that can be safely
@@ -1664,54 +1656,15 @@ export function mergeMilestoneToMain(
     }
   }
 
-  // 7. Stash any pre-existing dirty files so the squash merge is not
-  //    blocked by unrelated local changes (#2151).  clearProjectRootStateFiles
-  //    only removes untracked .gsd/ files; tracked dirty files elsewhere (e.g.
-  //    .planning/work-state.json with stash conflict markers) are invisible to
-  //    that cleanup but will cause `git merge --squash` to reject.
-  let stashed = false;
-  try {
-    const status = execFileSync("git", ["status", "--porcelain"], {
-      cwd: originalBasePath_,
-      stdio: ["ignore", "pipe", "pipe"],
-      encoding: "utf-8",
-    }).trim();
-    if (status) {
-      // Use --include-untracked to stash untracked files that would block
-      // the squash merge, but EXCLUDE .gsd/milestones/ (#2505).
-      // --include-untracked without exclusion sweeps queued milestone
-      // CONTEXT files into the stash. If stash pop later fails, those files
-      // are permanently trapped in the stash entry and lost on the next
-      // stash push or drop.
-      //
-      // When `.gsd` itself is a symlink, Git rejects pathspecs below it
-      // ("beyond a symbolic link"). In that layout, exclude the whole symlink
-      // and keep stashing real project files that could block the merge.
-      const stashPathspecs = isProjectGsdSymlink(originalBasePath_)
-        ? [".", ":(exclude).gsd"]
-        : [":(exclude).gsd/milestones"];
-      execFileSync(
-        "git",
-        [
-          "stash", "push", "--include-untracked",
-          "-m", `gsd: pre-merge stash for ${milestoneId}`,
-          "--", ...stashPathspecs,
-        ],
-        { cwd: originalBasePath_, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" },
-      );
-      stashed = true;
-    }
-  } catch (err) {
-    // Stash failure is non-fatal — proceed without stash and let the merge
-    // report the dirty tree if it fails.
-    logWarning("worktree", `git stash failed: ${err instanceof Error ? err.message : String(err)}`);
-  }
-
-  // 7a. Shelter queued milestone directories before the squash merge (#2505).
+  // 7. Shelter queued milestone directories before the squash merge (#2505).
   // The milestone branch may contain copies of queued milestone dirs (via
   // copyPlanningArtifacts), so `git merge --squash` rejects when those same
   // files exist as untracked in the working tree. Temporarily move them to
   // a backup location, then restore after the merge+commit.
+  //
+  // MUST run BEFORE the pre-merge stash (step 7a) so `--include-untracked`
+  // does not sweep queued CONTEXT files into the stash. If stash pop later
+  // fails, files trapped inside the stash are permanently lost (#2505).
   const milestonesDir = join(gsdRoot(originalBasePath_), "milestones");
   const shelterDir = join(gsdRoot(originalBasePath_), ".milestone-shelter");
   const shelteredDirs: string[] = [];
@@ -1759,6 +1712,35 @@ export function mergeMilestoneToMain(
     logWarning("worktree", `milestone shelter operation failed: ${err instanceof Error ? err.message : String(err)}`);
   }
 
+  // 7a. Stash pre-existing dirty files so the squash merge is not blocked by
+  //     unrelated local changes (#2151). Includes untracked files to handle
+  //     locally-added files that conflict with tracked files on the milestone
+  //     branch. Passing NO pathspec lets git skip gitignored paths silently;
+  //     adding an explicit pathspec trips a `git add`-style fatal on ignored
+  //     entries (e.g. a gitignored `.gsd` symlink under ADR-002) (#4573).
+  //     Queued CONTEXT files under `.gsd/milestones/*` are already sheltered
+  //     in step 7 above, so they won't be swept into the stash.
+  let stashed = false;
+  try {
+    const status = execFileSync("git", ["status", "--porcelain"], {
+      cwd: originalBasePath_,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+    }).trim();
+    if (status) {
+      execFileSync(
+        "git",
+        ["stash", "push", "--include-untracked", "-m", `gsd: pre-merge stash for ${milestoneId}`],
+        { cwd: originalBasePath_, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" },
+      );
+      stashed = true;
+    }
+  } catch (err) {
+    // Stash failure is non-fatal — proceed without stash and let the merge
+    // report the dirty tree if it fails.
+    logWarning("worktree", `git stash failed: ${err instanceof Error ? err.message : String(err)}`);
+  }
+
   // 7b. Clean up stale merge state before attempting squash merge (#2912).
   // A leftover MERGE_HEAD (from a previous failed merge, libgit2 native path,
   // or interrupted operation) causes `git merge --squash` to refuse with
@@ -2012,21 +1994,38 @@ export function mergeMilestoneToMain(
   // When a milestone only produced .gsd/ metadata (summaries, roadmaps) but no
   // real code, the user sees "milestone complete" but nothing changed in their
   // codebase. Surface this so the caller can warn the user.
+  //
+  // Bug #4385 fix: use `git diff-tree --root` instead of `git diff HEAD~1 HEAD`.
+  // `HEAD~1` does not exist on initial commits and is unreliable on shallow clones
+  // and merge commits. `diff-tree --root` handles all three cases correctly.
+  // The empty-tree hash (4b825dc…) is the universal fallback for refs that don't exist.
+  const GIT_EMPTY_TREE = "4b825dc642cb6eb9a060e54bf8d69288fbee4904";
   let codeFilesChanged = false;
   if (!nothingToCommit) {
     try {
-      const mergedFiles = nativeDiffNumstat(
-        originalBasePath_,
-        "HEAD~1",
-        "HEAD",
-      );
-      codeFilesChanged = mergedFiles.some(
-        (entry) => !entry.path.startsWith(".gsd/"),
-      );
+      const diffTreeOutput = execFileSync(
+        "git",
+        ["diff-tree", "--root", "--no-commit-id", "-r", "--name-only", "HEAD"],
+        { cwd: originalBasePath_, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" },
+      ).trim();
+      const mergedFiles = diffTreeOutput ? diffTreeOutput.split("\n").filter(Boolean) : [];
+      codeFilesChanged = mergedFiles.some((f) => !f.startsWith(".gsd/"));
     } catch (e) {
-      // If HEAD~1 doesn't exist (first commit), assume code was changed
-      logWarning("worktree", `diff numstat failed (assuming code changed): ${(e as Error).message}`);
-      codeFilesChanged = true;
+      // diff-tree failed (e.g. unborn HEAD in a brand-new repo) — fall back to
+      // comparing against the empty tree so initial-commit repos still report changes.
+      try {
+        const fallbackOutput = execFileSync(
+          "git",
+          ["diff", "--name-only", GIT_EMPTY_TREE, "HEAD"],
+          { cwd: originalBasePath_, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" },
+        ).trim();
+        const fallbackFiles = fallbackOutput ? fallbackOutput.split("\n").filter(Boolean) : [];
+        codeFilesChanged = fallbackFiles.some((f) => !f.startsWith(".gsd/"));
+      } catch {
+        // Truly unable to determine — assume code was changed to avoid silent data loss
+        logWarning("worktree", `diff-tree and empty-tree fallback both failed (assuming code changed): ${(e as Error).message}`);
+        codeFilesChanged = true;
+      }
     }
   }
 

package/src/resources/extensions/gsd/auto.ts

@@ -126,8 +126,9 @@ import {
   formatTokenCount,
 } from "./metrics.js";
 import { setLogBasePath, logWarning, logError } from "./workflow-logger.js";
+import { preflightCleanRoot, postflightPopStash } from "./clean-root-preflight.js";
 import { homedir } from "node:os";
-import { join } from "node:path";
+import { isAbsolute, join } from "node:path";
 import { pathToFileURL } from "node:url";
 import { readFileSync, existsSync, mkdirSync, writeFileSync, unlinkSync } from "node:fs";
 import { atomicWriteSync } from "./atomic-write.js";
@@ -182,7 +183,6 @@ import {
   unitVerb,
   formatAutoElapsed as _formatAutoElapsed,
   formatWidgetTokens,
-  hideFooter,
   type WidgetStateAccessors,
 } from "./auto-dashboard.js";
 import {
@@ -310,6 +310,21 @@ function restoreMilestoneLockEnv(): void {
   s.milestoneLockEnvCaptured = false;
 }
 
+function normalizeSessionFilePath(raw: unknown): string | null {
+  if (typeof raw !== "string") return null;
+  const trimmed = raw.trim();
+  if (!trimmed) return null;
+  const firstLine = trimmed.split(/\r?\n/, 1)[0]?.trim() ?? "";
+  if (!firstLine) return null;
+
+  // Guard against accidental message concatenation by trimming to .jsonl.
+  const jsonlIndex = firstLine.toLowerCase().indexOf(".jsonl");
+  const candidate = jsonlIndex >= 0 ? firstLine.slice(0, jsonlIndex + ".jsonl".length) : firstLine;
+  if (!isAbsolute(candidate)) return null;
+  if (!candidate.toLowerCase().endsWith(".jsonl")) return null;
+  return candidate;
+}
+
 export function startAutoDetached(
   ctx: ExtensionCommandContext,
   pi: ExtensionAPI,
@@ -330,8 +345,8 @@ export function startAutoDetached(
 }
 
 /** Returns true if the project is configured for `isolation:worktree` mode. */
-export function shouldUseWorktreeIsolation(): boolean {
-  const prefs = loadEffectiveGSDPreferences()?.preferences?.git;
+export function shouldUseWorktreeIsolation(basePath?: string): boolean {
+  const prefs = loadEffectiveGSDPreferences(basePath)?.preferences?.git;
   if (prefs?.isolation === "worktree") return true;
   // Default is false — worktree isolation requires explicit opt-in
   return false;
@@ -424,7 +439,7 @@ export function getAutoDashboardData(): AutoDashboardData {
   const rtkSavings = sessionId && s.basePath
     ? getRtkSessionSavings(s.basePath, sessionId)
     : null;
-  const rtkEnabled = loadEffectiveGSDPreferences()?.preferences.experimental?.rtk === true;
+  const rtkEnabled = loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences.experimental?.rtk === true;
   // Pending capture count — lazy check, non-fatal
   let pendingCaptureCount = 0;
   try {
@@ -648,7 +663,7 @@ function buildSnapshotOpts(
   gitStatus?: "ok" | "failed";
   gitError?: string;
 } & Record<string, unknown> {
-  const prefs = loadEffectiveGSDPreferences()?.preferences;
+  const prefs = loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences;
   const uokFlags = resolveUokFlags(prefs);
   return {
     ...(s.autoStartTime > 0 ? { autoSessionKey: String(s.autoStartTime) } : {}),
@@ -686,7 +701,7 @@ function handleLostSessionLock(
   restoreProjectRootEnv();
   restoreMilestoneLockEnv();
   deregisterSigtermHandler();
-  clearCmuxSidebar(loadEffectiveGSDPreferences()?.preferences);
+  clearCmuxSidebar(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences);
   const base = lockBase();
   const lockFilePath = base ? join(gsdRoot(base), "auto.lock") : "unknown";
   const recoverySuggestion = "\nTo recover, run: gsd doctor --fix";
@@ -706,7 +721,6 @@ function handleLostSessionLock(
   );
   ctx?.ui.setStatus("gsd-auto", undefined);
   ctx?.ui.setWidget("gsd-progress", undefined);
-  ctx?.ui.setFooter(undefined);
   if (ctx) initHealthWidget(ctx);
 }
 
@@ -742,7 +756,6 @@ function cleanupAfterLoopExit(ctx: ExtensionContext): void {
   if (!s.paused) {
     ctx.ui.setStatus("gsd-auto", undefined);
     ctx.ui.setWidget("gsd-progress", undefined);
-    ctx.ui.setFooter(undefined);
     initHealthWidget(ctx);
   }
 
@@ -764,7 +777,7 @@ export async function stopAuto(
   reason?: string,
 ): Promise<void> {
   if (!s.active && !s.paused) return;
-  const loadedPreferences = loadEffectiveGSDPreferences()?.preferences;
+  const loadedPreferences = loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences;
   const reasonSuffix = reason ? ` — ${reason}` : "";
 
   try {
@@ -969,7 +982,7 @@ export async function stopAuto(
       logWarning("engine", `file unlink failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
     }
 
-    // ── Step 13: Restore original model (before reset clears IDs) ──
+    // ── Step 13: Restore original model + thinking (before reset clears IDs) ──
     try {
       if (pi && ctx && s.originalModelId && s.originalModelProvider) {
         const original = ctx.modelRegistry.find(
@@ -978,6 +991,9 @@ export async function stopAuto(
         );
         if (original) await pi.setModel(original);
       }
+      if (pi && s.originalThinkingLevel) {
+        pi.setThinkingLevel(s.originalThinkingLevel);
+      }
     } catch (e) {
       debugLog("stop-cleanup-model", { error: e instanceof Error ? e.message : String(e) });
     }
@@ -1015,7 +1031,6 @@ export async function stopAuto(
     // UI cleanup
     ctx?.ui.setStatus("gsd-auto", undefined);
     ctx?.ui.setWidget("gsd-progress", undefined);
-    ctx?.ui.setFooter(undefined);
     if (ctx) initHealthWidget(ctx);
     restoreProjectRootEnv();
     restoreMilestoneLockEnv();
@@ -1056,7 +1071,7 @@ export async function pauseAuto(
   // from provider-error pause and avoid hard-stopping (#2762).
   resolveAgentEndCancelled(_errorContext);
 
-  s.pausedSessionFile = ctx?.sessionManager?.getSessionFile() ?? null;
+  s.pausedSessionFile = normalizeSessionFilePath(ctx?.sessionManager?.getSessionFile() ?? null);
 
   // Persist paused-session metadata so resume survives /exit (#1383).
   // The fresh-start bootstrap checks for this file and restores worktree context.
@@ -1118,7 +1133,6 @@ export async function pauseAuto(
   s.verificationRetryCount.clear();
   ctx?.ui.setStatus("gsd-auto", "paused");
   ctx?.ui.setWidget("gsd-progress", undefined);
-  ctx?.ui.setFooter(undefined);
   if (ctx) initHealthWidget(ctx);
   const resumeCmd = s.stepMode ? "/gsd next" : "/gsd auto";
   ctx?.ui.notify(
@@ -1289,6 +1303,10 @@ function buildLoopDeps(): LoopDeps {
 
     // Journal
     emitJournalEvent: (entry: JournalEntry) => _emitJournalEvent(s.basePath, entry),
+
+    // Clean-root preflight gate (#2909)
+    preflightCleanRoot,
+    postflightPopStash,
   } as unknown as LoopDeps;
 }
 
@@ -1361,7 +1379,11 @@ export async function startAuto(
         s.autoStartTime = meta.autoStartTime || Date.now();
         s.sessionMilestoneLock = meta.milestoneLock ?? null;
         s.paused = true;
-        try { unlinkSync(pausedPath); } catch (e) { logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" }); }
+        try { unlinkSync(pausedPath); } catch (e) {
+          if ((e as NodeJS.ErrnoException).code !== "ENOENT") {
+            logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+          }
+        }
         ctx.ui.notify(
           `Resuming paused custom workflow${meta.activeRunDir ? ` (${meta.activeRunDir})` : ""}.`,
           "info",
@@ -1380,7 +1402,9 @@ export async function startAuto(
           const summaryFile = resolveMilestoneFile(base, meta.milestoneId, "SUMMARY");
           if (!mDir || summaryFile) {
             try { unlinkSync(pausedPath); } catch (err) {
-              logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+              if ((err as NodeJS.ErrnoException).code !== "ENOENT") {
+                logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+              }
             }
             ctx.ui.notify(
               `Paused milestone ${meta.milestoneId} is ${!mDir ? "missing" : "already complete"}. Starting fresh.`,
@@ -1390,20 +1414,28 @@ export async function startAuto(
             s.currentMilestoneId = meta.milestoneId;
             s.originalBasePath = meta.originalBasePath || base;
             s.stepMode = meta.stepMode ?? requestedStepMode;
-            s.pausedSessionFile = meta.sessionFile ?? null;
+            s.pausedSessionFile = normalizeSessionFilePath(meta.sessionFile ?? null);
             s.pausedUnitType = meta.unitType ?? null;
             s.pausedUnitId = meta.unitId ?? null;
             s.autoStartTime = meta.autoStartTime || Date.now();
             s.sessionMilestoneLock = meta.milestoneLock ?? null;
             s.paused = true;
-            try { unlinkSync(pausedPath); } catch (e) { logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" }); }
+            try { unlinkSync(pausedPath); } catch (e) {
+              if ((e as NodeJS.ErrnoException).code !== "ENOENT") {
+                logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+              }
+            }
             ctx.ui.notify(
               `Resuming paused session for ${meta.milestoneId}${meta.worktreePath && existsSync(meta.worktreePath) ? ` (worktree)` : ""}.`,
               "info",
             );
           }
         } else if (existsSync(pausedPath)) {
-          try { unlinkSync(pausedPath); } catch (e) { logWarning("session", `stale pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" }); }
+          try { unlinkSync(pausedPath); } catch (e) {
+            if ((e as NodeJS.ErrnoException).code !== "ENOENT") {
+              logWarning("session", `stale pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+            }
+          }
         }
       }
     } catch (err) {
@@ -1462,7 +1494,9 @@ export async function startAuto(
     // Lock acquired — now safe to delete the pause file
     if (s.pausedSessionFile) {
       try { unlinkSync(s.pausedSessionFile); } catch (err) {
-        logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+        if ((err as NodeJS.ErrnoException).code !== "ENOENT") {
+          logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+        }
       }
       s.pausedSessionFile = null;
     }
@@ -1473,6 +1507,17 @@ export async function startAuto(
     s.stepMode = requestedStepMode;
     s.cmdCtx = ctx;
     s.basePath = base;
+    // ── Resume worktree: if the paused session was inside a milestone worktree,
+    // apply that path as the dispatch basePath immediately (#3723).
+    // This ensures the dispatch loop runs from the worktree directory even when
+    // enterMilestone guard conditions differ between the original and resumed
+    // session (e.g. isolation mode changed, detectWorktreeName differs across
+    // process restarts).  We guard with existsSync so a stale or deleted
+    // worktree directory safely falls back to the project root.
+    const resumeWorktreePath = freshStartAssessment.pausedSession?.worktreePath;
+    if (resumeWorktreePath && existsSync(resumeWorktreePath)) {
+      s.basePath = resumeWorktreePath;
+    }
     // Ensure the workflow-logger audit log is pinned to the project root
     // even when auto-mode is entered via a path that bypasses the
     // bootstrap/dynamic-tools ensureDbOpen() → setLogBasePath() chain
@@ -1492,7 +1537,7 @@ export async function startAuto(
     // ── Auto-worktree / branch-mode: re-enter on resume ──
     if (
       s.currentMilestoneId &&
-      getIsolationMode() !== "none" &&
+      getIsolationMode(s.originalBasePath || s.basePath) !== "none" &&
       s.originalBasePath &&
       !isInAutoWorktree(s.basePath) &&
       !detectWorktreeName(s.basePath) &&
@@ -1506,7 +1551,7 @@ export async function startAuto(
     registerSigtermHandler(lockBase());
 
     ctx.ui.setStatus("gsd-auto", s.stepMode ? "next" : "auto");
-    ctx.ui.setFooter(hideFooter);
+    ctx.ui.setWidget("gsd-health", undefined);
     ctx.ui.notify(
       s.stepMode ? "Step-mode resumed." : "Auto-mode resumed.",
       "info",
@@ -1531,7 +1576,7 @@ export async function startAuto(
     await openProjectDbIfPresent(s.basePath);
     try {
       await rebuildState(s.basePath);
-      syncCmuxSidebar(loadEffectiveGSDPreferences()?.preferences, await deriveState(s.basePath));
+      syncCmuxSidebar(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, await deriveState(s.basePath));
     } catch (e) {
       debugLog("resume-rebuild-state-failed", {
         error: e instanceof Error ? e.message : String(e),
@@ -1581,7 +1626,7 @@ export async function startAuto(
       "resuming",
       s.currentMilestoneId ?? "unknown",
     );
-    logCmuxEvent(loadEffectiveGSDPreferences()?.preferences, s.stepMode ? "Step-mode resumed." : "Auto-mode resumed.", "progress");
+    logCmuxEvent(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, s.stepMode ? "Step-mode resumed." : "Auto-mode resumed.", "progress");
 
     captureProjectRootEnv(s.originalBasePath || s.basePath);
     startAutoCommandPolling(s.basePath);
@@ -1619,12 +1664,12 @@ export async function startAuto(
 
   captureProjectRootEnv(s.originalBasePath || s.basePath);
   try {
-    syncCmuxSidebar(loadEffectiveGSDPreferences()?.preferences, await deriveState(s.basePath));
+    syncCmuxSidebar(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, await deriveState(s.basePath));
   } catch (err) {
     // Best-effort only — sidebar sync must never block auto-mode startup
     logWarning("engine", `cmux sync failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
   }
-  logCmuxEvent(loadEffectiveGSDPreferences()?.preferences, requestedStepMode ? "Step-mode started." : "Auto-mode started.", "progress");
+  logCmuxEvent(loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, requestedStepMode ? "Step-mode started." : "Auto-mode started.", "progress");
 
   startAutoCommandPolling(s.basePath);
 
@@ -1773,12 +1818,12 @@ export async function dispatchHookUnit(
     }
   }
 
-  const sessionFile = ctx.sessionManager.getSessionFile();
+  const sessionFile = normalizeSessionFilePath(ctx.sessionManager.getSessionFile());
   writeLock(
     lockBase(),
     hookUnitType,
     triggerUnitId,
-    sessionFile,
+    sessionFile ?? undefined,
   );
 
   clearUnitTimeout();

package/src/resources/extensions/gsd/bootstrap/agent-end-recovery.ts

@@ -1,7 +1,12 @@
 import type { ExtensionAPI, ExtensionContext } from "@gsd/pi-coding-agent";
 
 import { logWarning } from "../workflow-logger.js";
-import { checkAutoStartAfterDiscuss } from "../guided-flow.js";
+import {
+  checkAutoStartAfterDiscuss,
+  maybeHandleReadyPhraseWithoutFiles,
+  maybeHandleEmptyIntentTurn,
+  resetEmptyTurnCounter,
+} from "../guided-flow.js";
 import { getAutoDashboardData, getAutoModeStartModel, isAutoActive, pauseAuto, setCurrentDispatchedModelId } from "../auto.js";
 import { getNextFallbackModel, resolveModelWithFallbacksForUnit } from "../preferences.js";
 import { pauseAutoForProviderError } from "../provider-error-pause.js";
@@ -75,6 +80,20 @@ export async function handleAgentEnd(
     clearDiscussionFlowState();
     return;
   }
+
+  // #4573 — When the LLM emits "Milestone X ready." but the required files
+  // are missing, `checkAutoStartAfterDiscuss` returns false silently. Surface
+  // that and nudge the LLM to complete the writes before the user hits the
+  // downstream "All milestones complete" warning loop.
+  if (maybeHandleReadyPhraseWithoutFiles(event)) return;
+
+  // #4573 — Empty-turn recovery: if the LLM announced intent in prose but
+  // emitted no tool calls, nudge it to execute. Fires only when auto-mode is
+  // active or a discussion autostart is pending (non-auto interactive discuss
+  // is user-driven). Runs before `isAutoActive` early return so pending
+  // discussions (where isAutoActive may be false) still get recovered.
+  if (maybeHandleEmptyIntentTurn(event, isAutoActive())) return;
+
   if (!isAutoActive()) return;
   if (isSessionSwitchInFlight()) return;
 
@@ -336,6 +355,9 @@ export async function handleAgentEnd(
   // ── Success path ─────────────────────────────────────────────────────────
   try {
     resetRetryState(retryState);
+    // #4573 — Reset the empty-turn counter on any successful agent turn so
+    // transient stalls don't accumulate across independent units.
+    resetEmptyTurnCounter();
     resolveAgentEnd(event);
   } catch (err) {
     const message = err instanceof Error ? err.message : String(err);

package/src/resources/extensions/gsd/bootstrap/db-tools.ts

@@ -35,6 +35,19 @@ function registerAlias(pi: ExtensionAPI, toolDef: any, aliasName: string, canoni
   });
 }
 
+/**
+ * Read a tool result's structured payload, accommodating MCP's `details` →
+ * `structuredContent` rename (#4472, #4477). In-process executions still
+ * deliver the payload on `result.details`; MCP-routed executions deliver it
+ * on `result.structuredContent` (post `adaptExecutorResult` transform). All
+ * `renderResult` callbacks in this file route through this helper so a future
+ * field rename only needs to be applied in one place.
+ */
+// eslint-disable-next-line @typescript-eslint/no-explicit-any -- result shape varies by tool
+function readDetails(result: any): any {
+  return result?.details ?? result?.structuredContent;
+}
+
 export function registerDbTools(pi: ExtensionAPI): void {
   // ─── gsd_decision_save (formerly gsd_save_decision) ─────────────────────
 
@@ -110,7 +123,7 @@ export function registerDbTools(pi: ExtensionAPI): void {
       return new Text(text, 0, 0);
     },
     renderResult(result: any, _options: any, theme: any) {
-      const d = result.details;
+      const d = readDetails(result);
       if (result.isError || d?.error) {
         return new Text(theme.fg("error", `Error: ${d?.error ?? "unknown"}`), 0, 0);
       }
@@ -188,7 +201,7 @@ export function registerDbTools(pi: ExtensionAPI): void {
       return new Text(text, 0, 0);
     },
     renderResult(result: any, _options: any, theme: any) {
-      const d = result.details;
+      const d = readDetails(result);
       if (result.isError || d?.error) {
         return new Text(theme.fg("error", `Error: ${d?.error ?? "unknown"}`), 0, 0);
       }
@@ -273,7 +286,7 @@ export function registerDbTools(pi: ExtensionAPI): void {
       return new Text(text, 0, 0);
     },
     renderResult(result: any, _options: any, theme: any) {
-      const d = result.details;
+      const d = readDetails(result);
       if (result.isError || d?.error) {
         return new Text(theme.fg("error", `Error: ${d?.error ?? "unknown"}`), 0, 0);
       }
@@ -322,7 +335,7 @@ export function registerDbTools(pi: ExtensionAPI): void {
       return new Text(text, 0, 0);
     },
     renderResult(result: any, _options: any, theme: any) {
-      const d = result.details;
+      const d = readDetails(result);
       if (result.isError || d?.error) {
         return new Text(theme.fg("error", `Error: ${d?.error ?? "unknown"}`), 0, 0);
       }
@@ -406,7 +419,7 @@ export function registerDbTools(pi: ExtensionAPI): void {
       return new Text(theme.fg("toolTitle", theme.bold("milestone_generate_id")), 0, 0);
     },
     renderResult(result: any, _options: any, theme: any) {
-      const d = result.details;
+      const d = readDetails(result);
       if (result.isError || d?.error) {
         return new Text(theme.fg("error", `Error: ${d?.error ?? "unknown"}`), 0, 0);
       }
@@ -1074,13 +1087,31 @@ export function registerDbTools(pi: ExtensionAPI): void {
       text += theme.fg("dim", ` → ${args.verdict ?? ""}`);
       return new Text(text, 0, 0);
     },
+    /**
+     * Render the save_gate_result tool output for the TUI.
+     *
+     * Prefers structured fields, but falls back to `content[0].text` when the
+     * structured payload is empty. Defensive: the structural fix on this
+     * branch plumbs `details` through MCP via `structuredContent`, but older
+     * hosts, a future handler that forgets `structuredContent`, or any drop
+     * of non-standard return fields would otherwise render as
+     * "undefined: undefined". Same fallback applies to error rendering, and
+     * we strip a leading `Error:` from the fallback text to avoid producing
+     * `Error: Error: ...`.
+     */
     renderResult(result: any, _options: any, theme: any) {
-      const d = result.details;
+      const d = readDetails(result);
       if (result.isError || d?.error) {
-        return new Text(theme.fg("error", `Error: ${d?.error ?? "unknown"}`), 0, 0);
+        const rawMsg = d?.error ?? result.content?.[0]?.text ?? "unknown";
+        const msg = rawMsg.replace(/^\s*Error:\s*/i, "");
+        return new Text(theme.fg("error", `Error: ${msg}`), 0, 0);
+      }
+      if (!d?.gateId || !d?.verdict) {
+        const text = result.content?.[0]?.text ?? "Gate result saved";
+        return new Text(theme.fg("success", text), 0, 0);
       }
-      const color = d?.verdict === "flag" ? "warning" : "success";
-      return new Text(theme.fg(color, `${d?.gateId}: ${d?.verdict}`), 0, 0);
+      const color = d.verdict === "flag" ? "warning" : "success";
+      return new Text(theme.fg(color, `${d.gateId}: ${d.verdict}`), 0, 0);
     },
   };