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

package/dist/resources/extensions/gsd/auto-worktree.js

@@ -180,14 +180,6 @@ function clearProjectRootStateFiles(basePath, milestoneId) {
         }
     }
 }
-function isProjectGsdSymlink(basePath) {
-    try {
-        return lstatSyncFn(join(basePath, ".gsd")).isSymbolicLink();
-    }
-    catch {
-        return false;
-    }
-}
 // ─── Build Artifact Auto-Resolve ─────────────────────────────────────────────
 /** Patterns for machine-generated build artifacts that can be safely
  * auto-resolved by accepting --theirs during merge. These files are
@@ -1429,50 +1421,15 @@ export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapCont
             });
         }
     }
-    // 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 = [];
@@ -1526,6 +1483,31 @@ export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapCont
         // Non-fatal — proceed with merge; untracked files may block it
         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
@@ -1761,16 +1743,32 @@ export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapCont
     // 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.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.message}`);
+                codeFilesChanged = true;
+            }
         }
     }
     // 10. Auto-push if enabled

package/dist/resources/extensions/gsd/auto.js

@@ -37,8 +37,9 @@ import { getRtkSessionSavings } from "../shared/rtk-session-stats.js";
 import { deactivateGSD } from "../shared/gsd-phase-state.js";
 import { initMetrics, resetMetrics, getLedger, getProjectTotals, formatCost, formatTokenCount, } from "./metrics.js";
 import { setLogBasePath, logWarning } 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";
@@ -55,7 +56,7 @@ import { getErrorMessage } from "./error-utils.js";
 import { recoverFailedMigration } from "./migrate-external.js";
 import { initRegistry, convertDispatchRules } from "./rule-registry.js";
 import { emitJournalEvent as _emitJournalEvent } from "./journal.js";
-import { updateProgressWidget as _updateProgressWidget, updateSliceProgressCache, clearSliceProgressCache, hideFooter, } from "./auto-dashboard.js";
+import { updateProgressWidget as _updateProgressWidget, updateSliceProgressCache, clearSliceProgressCache, } from "./auto-dashboard.js";
 import { registerSigtermHandler as _registerSigtermHandler, deregisterSigtermHandler as _deregisterSigtermHandler, } from "./auto-supervisor.js";
 import { isDbAvailable, getMilestone } from "./gsd-db.js";
 import { countPendingCaptures } from "./captures.js";
@@ -136,6 +137,24 @@ function restoreMilestoneLockEnv() {
     s.hadMilestoneLockEnv = false;
     s.milestoneLockEnvCaptured = false;
 }
+function normalizeSessionFilePath(raw) {
+    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, pi, base, verboseMode, options) {
     void startAuto(ctx, pi, base, verboseMode, options).catch((err) => {
         const message = getErrorMessage(err);
@@ -145,8 +164,8 @@ export function startAutoDetached(ctx, pi, base, verboseMode, options) {
     });
 }
 /** Returns true if the project is configured for `isolation:worktree` mode. */
-export function shouldUseWorktreeIsolation() {
-    const prefs = loadEffectiveGSDPreferences()?.preferences?.git;
+export function shouldUseWorktreeIsolation(basePath) {
+    const prefs = loadEffectiveGSDPreferences(basePath)?.preferences?.git;
     if (prefs?.isolation === "worktree")
         return true;
     // Default is false — worktree isolation requires explicit opt-in
@@ -215,7 +234,7 @@ export function getAutoDashboardData() {
     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 {
@@ -393,7 +412,7 @@ function clearUnitTimeout() {
 }
 /** Build snapshot metric opts. */
 function buildSnapshotOpts(_unitType, _unitId) {
-    const prefs = loadEffectiveGSDPreferences()?.preferences;
+    const prefs = loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences;
     const uokFlags = resolveUokFlags(prefs);
     return {
         ...(s.autoStartTime > 0 ? { autoSessionKey: String(s.autoStartTime) } : {}),
@@ -427,7 +446,7 @@ function handleLostSessionLock(ctx, lockStatus) {
     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";
@@ -443,7 +462,6 @@ function handleLostSessionLock(ctx, lockStatus) {
     ctx?.ui.notify(message, "error");
     ctx?.ui.setStatus("gsd-auto", undefined);
     ctx?.ui.setWidget("gsd-progress", undefined);
-    ctx?.ui.setFooter(undefined);
     if (ctx)
         initHealthWidget(ctx);
 }
@@ -480,7 +498,6 @@ function cleanupAfterLoopExit(ctx) {
     if (!s.paused) {
         ctx.ui.setStatus("gsd-auto", undefined);
         ctx.ui.setWidget("gsd-progress", undefined);
-        ctx.ui.setFooter(undefined);
         initHealthWidget(ctx);
     }
     // Restore CWD out of worktree back to original project root
@@ -498,7 +515,7 @@ function cleanupAfterLoopExit(ctx) {
 export async function stopAuto(ctx, pi, reason) {
     if (!s.active && !s.paused)
         return;
-    const loadedPreferences = loadEffectiveGSDPreferences()?.preferences;
+    const loadedPreferences = loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences;
     const reasonSuffix = reason ? ` — ${reason}` : "";
     try {
         // ── Step 1: Timers and locks ──
@@ -695,13 +712,16 @@ export async function stopAuto(ctx, pi, reason) {
         catch (err) { /* non-fatal */
             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(s.originalModelProvider, s.originalModelId);
                 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) });
@@ -740,7 +760,6 @@ export async function stopAuto(ctx, pi, reason) {
         // UI cleanup
         ctx?.ui.setStatus("gsd-auto", undefined);
         ctx?.ui.setWidget("gsd-progress", undefined);
-        ctx?.ui.setFooter(undefined);
         if (ctx)
             initHealthWidget(ctx);
         restoreProjectRootEnv();
@@ -775,7 +794,7 @@ export async function pauseAuto(ctx, _pi, _errorContext) {
     // Pass errorContext so runUnitPhase can distinguish user-initiated pause
     // 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.
     try {
@@ -829,7 +848,6 @@ export async function pauseAuto(ctx, _pi, _errorContext) {
     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";
@@ -975,6 +993,9 @@ function buildLoopDeps() {
         },
         // Journal
         emitJournalEvent: (entry) => _emitJournalEvent(s.basePath, entry),
+        // Clean-root preflight gate (#2909)
+        preflightCleanRoot,
+        postflightPopStash,
     };
 }
 /**
@@ -1031,7 +1052,9 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
                     unlinkSync(pausedPath);
                 }
                 catch (e) {
-                    logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+                    if (e.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");
             }
@@ -1049,7 +1072,9 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
                             unlinkSync(pausedPath);
                         }
                         catch (err) {
-                            logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+                            if (err.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.`, "info");
                     }
@@ -1057,7 +1082,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
                         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();
@@ -1067,7 +1092,9 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
                             unlinkSync(pausedPath);
                         }
                         catch (e) {
-                            logWarning("session", `pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+                            if (e.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");
                     }
@@ -1077,7 +1104,9 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
                         unlinkSync(pausedPath);
                     }
                     catch (e) {
-                        logWarning("session", `stale pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+                        if (e.code !== "ENOENT") {
+                            logWarning("session", `stale pause file cleanup failed: ${e instanceof Error ? e.message : String(e)}`, { file: "auto.ts" });
+                        }
                     }
                 }
             }
@@ -1133,7 +1162,9 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
                 unlinkSync(s.pausedSessionFile);
             }
             catch (err) {
-                logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+                if (err.code !== "ENOENT") {
+                    logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
+                }
             }
             s.pausedSessionFile = null;
         }
@@ -1143,6 +1174,17 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         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
@@ -1161,7 +1203,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         });
         // ── 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) &&
@@ -1172,7 +1214,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         }
         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");
         restoreHookState(s.basePath);
         // Re-sync managed resources on resume so long-lived auto sessions pick up
@@ -1194,7 +1236,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         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", {
@@ -1224,7 +1266,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         }
         updateSessionLock(lockBase(), "resuming", s.currentMilestoneId ?? "unknown");
         writeLock(lockBase(), "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);
         await runAutoLoopWithUok({
@@ -1250,13 +1292,13 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         return;
     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);
     // Dispatch the first unit
     await runAutoLoopWithUok({
@@ -1361,8 +1403,8 @@ export async function dispatchHookUnit(ctx, pi, hookName, triggerUnitType, trigg
                 `Ensure the model is defined in models.json and has auth configured.`, "warning");
         }
     }
-    const sessionFile = ctx.sessionManager.getSessionFile();
-    writeLock(lockBase(), hookUnitType, triggerUnitId, sessionFile);
+    const sessionFile = normalizeSessionFilePath(ctx.sessionManager.getSessionFile());
+    writeLock(lockBase(), hookUnitType, triggerUnitId, sessionFile ?? undefined);
     clearUnitTimeout();
     const supervisor = resolveAutoSupervisorConfig();
     const hookHardTimeoutMs = (supervisor.hard_timeout_minutes ?? 30) * 60 * 1000;

package/dist/resources/extensions/gsd/bootstrap/agent-end-recovery.js

@@ -1,5 +1,5 @@
 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";
@@ -53,6 +53,19 @@ export async function handleAgentEnd(pi, event, ctx) {
         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())
@@ -286,6 +299,9 @@ export async function handleAgentEnd(pi, event, ctx) {
     // ── 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) {

package/dist/resources/extensions/gsd/bootstrap/db-tools.js

@@ -19,6 +19,18 @@ function registerAlias(pi, toolDef, aliasName, canonicalName) {
         promptGuidelines: [`Alias for ${canonicalName} — prefer the canonical name.`],
     });
 }
+/**
+ * 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) {
+    return result?.details ?? result?.structuredContent;
+}
 export function registerDbTools(pi) {
     // ─── gsd_decision_save (formerly gsd_save_decision) ─────────────────────
     const decisionSaveExecute = async (_toolCallId, params, _signal, _onUpdate, _ctx) => {
@@ -92,7 +104,7 @@ export function registerDbTools(pi) {
             return new Text(text, 0, 0);
         },
         renderResult(result, _options, theme) {
-            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);
             }
@@ -175,7 +187,7 @@ export function registerDbTools(pi) {
             return new Text(text, 0, 0);
         },
         renderResult(result, _options, theme) {
-            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);
             }
@@ -255,7 +267,7 @@ export function registerDbTools(pi) {
             return new Text(text, 0, 0);
         },
         renderResult(result, _options, theme) {
-            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);
             }
@@ -301,7 +313,7 @@ export function registerDbTools(pi) {
             return new Text(text, 0, 0);
         },
         renderResult(result, _options, theme) {
-            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);
             }
@@ -382,7 +394,7 @@ export function registerDbTools(pi) {
             return new Text(theme.fg("toolTitle", theme.bold("milestone_generate_id")), 0, 0);
         },
         renderResult(result, _options, theme) {
-            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);
             }
@@ -967,13 +979,31 @@ export function registerDbTools(pi) {
             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, _options, theme) {
-            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);
         },
     };
     pi.registerTool(saveGateResultTool);