gsd-pi 2.82.0 → 3.0.0

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

@@ -252,7 +252,17 @@ function gitPathspecForWorktreePath(basePath: string, targetPath: string): strin
   let base = basePath;
   let target = targetPath;
   try {
-    base = realpathSync.native(basePath);
+    base = execFileSync("git", ["rev-parse", "--show-toplevel"], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "ignore"],
+      encoding: "utf-8",
+    }).trim() || basePath;
+  } catch {
+    /* keep original */
+    void base;
+  }
+  try {
+    base = realpathSync.native(base);
   } catch {
     /* keep original */
     void base;
@@ -269,6 +279,10 @@ function gitPathspecForWorktreePath(basePath: string, targetPath: string): strin
   return rel.replaceAll("\\", "/");
 }
 
+export function _gitPathspecForWorktreePath(basePath: string, targetPath: string): string | null {
+  return gitPathspecForWorktreePath(basePath, targetPath);
+}
+
 function gitRemoteExists(basePath: string, remote: string): boolean {
   try {
     execFileSync("git", ["remote", "get-url", remote], {
@@ -282,6 +296,50 @@ function gitRemoteExists(basePath: string, remote: string): boolean {
   }
 }
 
+function findRegularMergeChangedPaths(basePath: string, milestoneBranch: string, mainBranch: string): Set<string> {
+  const changedPaths = new Set<string>();
+  let mergeLog = "";
+  try {
+    mergeLog = execFileSync("git", ["rev-list", "--merges", "--parents", mainBranch], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+    }).trim();
+  } catch (err) {
+    logWarning("worktree", `regular merge lookup failed: ${err instanceof Error ? err.message : String(err)}`);
+    return changedPaths;
+  }
+
+  for (const line of mergeLog.split("\n").filter(Boolean)) {
+    const [mergeCommit, firstParent, ...otherParents] = line.split(" ");
+    if (!mergeCommit || !firstParent || otherParents.length === 0) continue;
+    const mergedMilestone = otherParents.some((parent) => {
+      try {
+        return nativeIsAncestor(basePath, milestoneBranch, parent);
+      } catch {
+        return false;
+      }
+    });
+    if (!mergedMilestone) continue;
+
+    try {
+      const output = execFileSync("git", ["diff", "--name-only", firstParent, mergeCommit], {
+        cwd: basePath,
+        stdio: ["ignore", "pipe", "pipe"],
+        encoding: "utf-8",
+      }).trim();
+      for (const path of output.split("\n").filter(Boolean)) {
+        if (!path.startsWith(".gsd/")) changedPaths.add(path);
+      }
+    } catch (err) {
+      logWarning("worktree", `regular merge diff lookup failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    return changedPaths;
+  }
+
+  return changedPaths;
+}
+
 function clearProjectRootStateFiles(basePath: string, milestoneId: string): void {
   const gsdDir = gsdRoot(basePath);
   // Phase C pt 2: auto.lock removed from this list — the file is gone
@@ -949,7 +1007,73 @@ export function enterBranchModeForMilestone(
     });
   }
 
-  nativeCheckoutBranch(basePath, branch);
+  checkoutBranchWithStashGuard(basePath, branch, `enter-branch-mode:${milestoneId}`);
+}
+
+export function checkoutBranchWithStashGuard(
+  basePath: string,
+  branch: string,
+  reason: string,
+): void {
+  let stashMarker: string | null = null;
+  let stashed = false;
+
+  const status = nativeWorkingTreeStatus(basePath).trim();
+  if (status.length > 0) {
+    stashMarker = `gsd-checkout-stash:${reason}:${process.pid}:${Date.now()}:${process.hrtime.bigint().toString(36)}`;
+    const stashListBefore = execFileSync("git", ["stash", "list"], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+    });
+    execFileSync(
+      "git",
+      ["stash", "push", "--include-untracked", "-m", `gsd: checkout stash [${stashMarker}]`],
+      {
+        cwd: basePath,
+        stdio: ["ignore", "pipe", "pipe"],
+        encoding: "utf-8",
+      },
+    );
+    const stashListAfter = execFileSync("git", ["stash", "list"], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+    });
+    stashed = stashListAfter !== stashListBefore;
+  }
+
+  // Checkout and stash-restore are split so we can distinguish two failure
+  // modes: (a) checkout failed → HEAD did not move, restore stash and rethrow;
+  // (b) checkout succeeded but stash pop failed → HEAD moved to `branch` but
+  // the working-tree changes remain in the stash list. We surface a distinct
+  // error in case (b) so callers don't assume the branch switch was rolled back.
+  try {
+    nativeCheckoutBranch(basePath, branch);
+  } catch (checkoutErr) {
+    if (stashed) {
+      try {
+        popStashByRef(basePath, stashMarker);
+      } catch (restoreErr) {
+        logWarning("worktree", `git stash pop failed during checkout restore: ${restoreErr instanceof Error ? restoreErr.message : String(restoreErr)}`);
+      }
+    }
+    throw checkoutErr;
+  }
+
+  if (stashed) {
+    try {
+      popStashByRef(basePath, stashMarker);
+    } catch (popErr) {
+      const msg = popErr instanceof Error ? popErr.message : String(popErr);
+      const wrapped = new Error(
+        `checkout to '${branch}' succeeded but stash restore failed; working tree changes remain in the stash list. Original error: ${msg}`,
+      );
+      const ref = (popErr as { stashRef?: string } | null)?.stashRef;
+      if (ref) (wrapped as { stashRef?: string }).stashRef = ref;
+      throw wrapped;
+    }
+  }
 }
 
 // ─── Public API ────────────────────────────────────────────────────────────
@@ -1739,6 +1863,66 @@ export function mergeMilestoneToMain(
     }
   }
 
+  // Already regular-merged milestones can skip the squash path and proceed to cleanup (#5831).
+  if (nativeIsAncestor(originalBasePath_, milestoneBranch, mainBranch)) {
+    const codeChanges = nativeDiffNumstat(
+      originalBasePath_,
+      mainBranch,
+      milestoneBranch,
+    ).filter((entry) => !entry.path.startsWith(".gsd/"));
+    if (codeChanges.length > 0) {
+      const regularMergeChangedPaths = findRegularMergeChangedPaths(
+        originalBasePath_,
+        milestoneBranch,
+        mainBranch,
+      );
+      const unanchoredCodeChanges = codeChanges.filter((entry) =>
+        regularMergeChangedPaths.has(entry.path)
+      );
+      if (unanchoredCodeChanges.length > 0) {
+        process.chdir(previousCwd);
+        throw new GSDError(
+          GSD_GIT_ERROR,
+          `Milestone branch "${milestoneBranch}" is reachable from "${mainBranch}" ` +
+            `but has ${unanchoredCodeChanges.length} milestone-touched code file(s) not on current "${mainBranch}". ` +
+            `Aborting worktree teardown to prevent data loss.`,
+        );
+      }
+    }
+    debugLog("mergeMilestoneToMain", {
+      action: "skip-squash-already-merged",
+      milestoneId,
+      milestoneBranch,
+      mainBranch,
+    });
+    try {
+      clearProjectRootStateFiles(originalBasePath_, milestoneId);
+    } catch (err) {
+      logWarning("worktree", `clearProjectRootStateFiles failed during already-merged cleanup: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    try {
+      removeWorktree(originalBasePath_, milestoneId, {
+        branch: milestoneBranch,
+        deleteBranch: false,
+      });
+    } catch (err) {
+      logWarning("worktree", `worktree removal failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    try {
+      nativeBranchDelete(originalBasePath_, milestoneBranch);
+    } catch (err) {
+      logWarning("worktree", `git branch-delete failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    setActiveWorkspace(null);
+    nudgeGitBranchCache(previousCwd);
+    try {
+      process.chdir(originalBasePath_);
+    } catch (err) {
+      logWarning("worktree", `chdir to project root after already-merged cleanup failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    return { commitMessage, pushed: false, prCreated: false, codeFilesChanged: true };
+  }
+
   // 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
@@ -1874,14 +2058,6 @@ export function mergeMilestoneToMain(
     logWarning("worktree", `git stash failed: ${err instanceof Error ? err.message : String(err)}`);
   }
 
-  if (needsDbCycle && dbPathToReopen) {
-    try {
-      openDatabase(dbPathToReopen);
-    } catch (err) {
-      logWarning("worktree", `post-stash db reopen 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
@@ -1891,6 +2067,13 @@ export function mergeMilestoneToMain(
 
   // 8. Squash merge — auto-resolve .gsd/ state file conflicts (#530)
   const mergeResult = nativeMergeSquash(originalBasePath_, milestoneBranch);
+  if (needsDbCycle && dbPathToReopen) {
+    try {
+      openDatabase(dbPathToReopen);
+    } catch (err) {
+      logWarning("worktree", `post-merge db reopen failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+  }
 
   if (!mergeResult.success) {
     // Dirty working tree — the merge was rejected before it started (e.g.

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

@@ -58,6 +58,7 @@ import {
 import {
   writeLock,
   clearLock,
+  clearStaleWorkerLock,
   readCrashLock,
   isLockProcessAlive,
   formatCrashInfo,
@@ -240,12 +241,14 @@ import { runAutoLoopWithUok } from "./uok/kernel.js";
 import { resolveUokFlags } from "./uok/flags.js";
 import { validateDirectory } from "./validate-directory.js";
 import { createAutoOrchestrator } from "./auto/orchestrator.js";
-import type { AutoOrchestrationModule, AutoOrchestratorDeps } from "./auto/contracts.js";
+import type { AutoAdvanceResult, AutoOrchestrationModule, AutoOrchestratorDeps, DispatchAdapter } from "./auto/contracts.js";
 import { reconcileBeforeDispatch } from "./state-reconciliation.js";
 import { compileUnitToolContract } from "./tool-contract.js";
 import { createWorktreeSafetyModule } from "./worktree-safety.js";
 import { resolveManifest } from "./unit-context-manifest.js";
 import { classifyFailure } from "./recovery-classification.js";
+import { supportsStructuredQuestions } from "./workflow-mcp.js";
+import type { MinimalModelRegistry } from "./context-budget.js";
 // Slice-level parallelism (#2340)
 import { getEligibleSlices } from "./slice-parallel-eligibility.js";
 import { startSliceParallel } from "./slice-parallel-orchestrator.js";
@@ -314,6 +317,13 @@ import { normalizeRealPath } from "./paths.js";
 /** Throttle STATE.md rebuilds — at most once per 30 seconds */
 const STATE_REBUILD_MIN_INTERVAL_MS = 30_000;
 
+export function formatAutoStopNotification(prefix: string, totals: { cost: number; tokens: { total: number } }, unitCount: number): string {
+  return [
+    `${prefix}.`,
+    `Session: ${formatCost(totals.cost)} · ${formatTokenCount(totals.tokens.total)} tokens · ${unitCount} units`,
+  ].join("\n");
+}
+
 /**
  * Phase B — register this auto-mode process in the workers table so other
  * workers and janitors can detect liveness via heartbeat. Best-effort: if
@@ -1019,6 +1029,8 @@ export async function rerootCommandSession(
 }
 
 export async function cleanupAfterLoopExit(ctx: ExtensionContext): Promise<void> {
+  const preserveStepSurface = s.preserveStepSurfaceAfterLoopExit;
+  const preservePausedSurface = s.paused;
   s.currentUnit = null;
   s.active = false;
   deactivateGSD();
@@ -1041,21 +1053,24 @@ export async function cleanupAfterLoopExit(ctx: ExtensionContext): Promise<void>
   // A transient provider-error pause intentionally leaves the paused badge
   // visible so the user still has a resumable auto-mode signal on screen.
   if (!s.paused) {
-    ctx.ui.setStatus("gsd-auto", undefined);
-    if (s.completionStopInProgress) {
-      s.completionStopInProgress = false;
+    if (preserveStepSurface) {
+      s.preserveStepSurfaceAfterLoopExit = false;
+    } else {
+      ctx.ui.setStatus("gsd-auto", undefined);
+      ctx.ui.setWidget("gsd-progress", undefined);
+      if (s.completionStopInProgress) {
+        s.completionStopInProgress = false;
+      }
+      initHealthWidget(ctx);
     }
-    initHealthWidget(ctx);
   }
 
-  // ADR-016 phase 3 (#5693): the stop-path basePath restore routes through
-  // `Lifecycle.restoreToProjectRoot()`, the sole owner of `s.basePath`
-  // mutation. The verb assigns `s.basePath` before any throwable work
-  // (rebuildGitService, cache invalidation), so a thrown error still leaves
-  // basePath restored — no fallback assignment needed at the call site.
-  // The chdir stays here because `restoreToProjectRoot` is a pure
-  // session-state mutation.
-  if (s.originalBasePath) {
+  // ADR-016 phase 3 (#5693): the stop-path basePath restore + chdir routes
+  // through `Lifecycle.restoreToProjectRoot()`, the sole owner of both
+  // `s.basePath` mutation and the paired `process.chdir` for auto-loop
+  // transitions. The verb assigns `s.basePath` before any throwable work, so
+  // a thrown error still leaves basePath restored.
+  if (s.originalBasePath && !preserveStepSurface && !preservePausedSurface) {
     try {
       buildLifecycle().restoreToProjectRoot();
     } catch (err) {
@@ -1065,14 +1080,9 @@ export async function cleanupAfterLoopExit(ctx: ExtensionContext): Promise<void>
         { file: "auto.ts" },
       );
     }
-    try {
-      process.chdir(s.originalBasePath);
-    } catch (err) {
-      logWarning("engine", `basePath restore/chdir failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
-    }
   }
 
-  if (s.originalBasePath && s.cmdCtx) {
+  if (s.originalBasePath && s.cmdCtx && !preserveStepSurface && !preservePausedSurface) {
     const result = await rerootCommandSession(s.cmdCtx, s.originalBasePath);
     if (result.status === "cancelled") {
       logWarning("engine", "post-loop session re-root was cancelled", { file: "auto.ts", basePath: s.originalBasePath });
@@ -1384,20 +1394,14 @@ export async function stopAuto(
     }
 
     // ── Step 7: Restore basePath and chdir (ADR-016 phase 3, #5693) ──
-    // `restoreToProjectRoot` assigns s.basePath before any throwable work;
-    // no fallback assignment is needed at the call site.
+    // `restoreToProjectRoot` owns both s.basePath restore and process.chdir;
+    // no paired chdir is needed at the call site.
     if (s.originalBasePath) {
       try {
         buildLifecycle().restoreToProjectRoot();
       } catch (e) {
         debugLog("stop-cleanup-basepath", { error: e instanceof Error ? e.message : String(e) });
       }
-      try {
-        process.chdir(s.basePath);
-      } catch (err) {
-        /* best-effort */
-        logWarning("engine", `chdir failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
-      }
     }
 
     // Re-root the active command session/tool runtime after worktree teardown.
@@ -1426,7 +1430,7 @@ export async function stopAuto(
       if (ledger && ledger.units.length > 0) {
         const totals = getProjectTotals(ledger.units);
         ctx?.ui.notify(
-          `${notificationPrefix}. Session: ${formatCost(totals.cost)} · ${formatTokenCount(totals.tokens.total)} tokens · ${ledger.units.length} units`,
+          formatAutoStopNotification(notificationPrefix, totals, ledger.units.length),
           "info",
         );
       } else {
@@ -1733,7 +1737,6 @@ export async function pauseAuto(
   restoreProjectRootEnv();
   restoreMilestoneLockEnv();
   s.pendingVerificationRetry = null;
-  s.verificationRetryCount.clear();
   ctx?.ui.setStatus("gsd-auto", "paused");
   ctx?.ui.setWidget("gsd-progress", undefined);
   const resumeCmd = s.stepMode ? "/gsd next" : "/gsd auto";
@@ -1792,6 +1795,82 @@ function buildLifecycle(): WorktreeLifecycle {
   return new WorktreeLifecycle(s, buildWorktreeLifecycleDeps());
 }
 
+/**
+ * Build the production `DispatchAdapter` used by `createWiredAutoOrchestrationModule`.
+ *
+ * Exported so tests can verify parity with `runDispatch`'s `resolveDispatch` call —
+ * the wired adapter must derive `structuredQuestionsAvailable`, `sessionContextWindow`,
+ * `sessionProvider`, and `modelRegistry` the same way phases.ts:runDispatch does.
+ */
+export function createWiredDispatchAdapter(
+  ctx: ExtensionContext,
+  pi: ExtensionAPI,
+  dispatchBasePath: string,
+): DispatchAdapter {
+  return {
+    async decideNextUnit(input) {
+      const state = input.stateSnapshot;
+      const active = state.activeMilestone;
+      if (!active) return null;
+
+      const prefs = loadEffectiveGSDPreferences(dispatchBasePath)?.preferences;
+
+      // Derive session-derived dispatch inputs the same way phases.ts:runDispatch does
+      // (#5789). Prefer caller-supplied values when present so test harnesses and
+      // alternative wirings can inject deterministic snapshots; otherwise pull from
+      // the captured pi/ctx references.
+      const sessionProvider = input.sessionProvider ?? ctx.model?.provider;
+      const sessionContextWindow = input.sessionContextWindow ?? ctx.model?.contextWindow;
+      const modelRegistry = input.modelRegistry ?? (ctx.modelRegistry as MinimalModelRegistry | undefined);
+      const authMode =
+        sessionProvider && typeof ctx.modelRegistry?.getProviderAuthMode === "function"
+          ? ctx.modelRegistry.getProviderAuthMode(sessionProvider)
+          : undefined;
+      const activeTools = typeof pi.getActiveTools === "function" ? pi.getActiveTools() : [];
+      // Mirrors runDispatch: deep-planning keeps approval gates in plain chat
+      // because structured questions can be cancelled outside the chat turn on
+      // some transports.
+      const structuredQuestionsAvailable =
+        input.structuredQuestionsAvailable ??
+        (prefs?.planning_depth === "deep"
+          ? "false"
+          : supportsStructuredQuestions(activeTools, {
+              authMode,
+              baseUrl: ctx.model?.baseUrl,
+            })
+            ? "true"
+            : "false");
+
+      const action = await resolveDispatch({
+        basePath: dispatchBasePath,
+        mid: active.id,
+        midTitle: active.title,
+        state,
+        prefs,
+        structuredQuestionsAvailable,
+        sessionContextWindow,
+        sessionProvider,
+        modelRegistry,
+      });
+
+      if (action.action === "stop") {
+        return {
+          kind: "blocked",
+          reason: action.reason,
+          action: action.level === "warning" ? "pause" : "stop",
+        };
+      }
+      if (action.action !== "dispatch") return null;
+      return {
+        unitType: action.unitType,
+        unitId: action.unitId,
+        reason: action.matchedRule ?? "dispatch",
+        preconditions: [],
+      };
+    },
+  };
+}
+
 /**
  * Thin entry glue for the new Auto Orchestration module.
  *
@@ -1801,7 +1880,7 @@ function buildLifecycle(): WorktreeLifecycle {
  */
 export function createWiredAutoOrchestrationModule(
   ctx: ExtensionContext,
-  _pi: ExtensionAPI,
+  pi: ExtensionAPI,
   dispatchBasePath: string,
   runtimeBasePath = resolveProjectRoot(dispatchBasePath),
 ): AutoOrchestrationModule {
@@ -1830,30 +1909,7 @@ export function createWiredAutoOrchestrationModule(
         };
       },
     },
-    dispatch: {
-      async decideNextUnit(input) {
-        const state = input.stateSnapshot;
-        const active = state.activeMilestone;
-        if (!active) return null;
-
-        const prefs = loadEffectiveGSDPreferences(dispatchBasePath)?.preferences;
-        const action = await resolveDispatch({
-          basePath: dispatchBasePath,
-          mid: active.id,
-          midTitle: active.title,
-          state,
-          prefs,
-        });
-
-        if (action.action !== "dispatch") return null;
-        return {
-          unitType: action.unitType,
-          unitId: action.unitId,
-          reason: action.matchedRule ?? "dispatch",
-          preconditions: [],
-        };
-      },
-    },
+    dispatch: createWiredDispatchAdapter(ctx, pi, dispatchBasePath),
     recovery: {
       async classifyAndRecover(input) {
         const recovery = classifyFailure(input);
@@ -1902,12 +1958,25 @@ export function createWiredAutoOrchestrationModule(
       async cleanupOnStop() {},
     },
     health: {
+      checkResourcesStale() {
+        return checkResourcesStale(s.resourceVersionOnStart);
+      },
       async preAdvanceGate() {
-        const gate = await preDispatchHealthGate(dispatchBasePath);
-        return {
-          allow: gate.proceed,
-          reason: gate.reason,
-        };
+        try {
+          const gate = await preDispatchHealthGate(dispatchBasePath);
+          if (gate.proceed) {
+            return {
+              kind: "pass",
+              fixesApplied: gate.fixesApplied,
+            };
+          }
+          return {
+            kind: "fail",
+            reason: gate.reason ?? "Pre-dispatch health check failed — run /gsd doctor for details.",
+          };
+        } catch (error) {
+          return { kind: "threw", error };
+        }
       },
       async postAdvanceRecord(result) {
         if (result.kind === "error") {
@@ -1975,11 +2044,60 @@ export function createWiredAutoOrchestrationModule(
         }
       },
     },
+    uokGate: {
+      async emit(input) {
+        const prefs = loadEffectiveGSDPreferences(dispatchBasePath)?.preferences;
+        const uokFlags = resolveUokFlags(prefs);
+        if (!uokFlags.gates) return;
+        const milestoneId = input.milestoneId ?? s.currentMilestoneId ?? undefined;
+        try {
+          const { UokGateRunner } = await import("./uok/gate-runner.js");
+          const runner = new UokGateRunner();
+          runner.register({
+            id: input.gateId,
+            type: input.gateType,
+            execute: async () => ({
+              outcome: input.outcome,
+              failureClass: input.failureClass,
+              rationale: input.rationale,
+              findings: input.findings ?? "",
+            }),
+          });
+          await runner.run(input.gateId, {
+            basePath: dispatchBasePath,
+            traceId: `pre-dispatch:${flowId}`,
+            turnId: `orch-${seq}`,
+            milestoneId,
+            unitType: "pre-dispatch",
+            unitId: `orch-${seq}`,
+          });
+        } catch (err) {
+          logWarning("engine", `uok gate emit failed: ${getErrorMessage(err)}`, {
+            file: "auto.ts",
+            gateId: input.gateId,
+            gateType: input.gateType,
+            ...(milestoneId ? { milestoneId } : {}),
+          });
+        }
+      },
+    },
   };
 
   return createAutoOrchestrator(deps);
 }
 
+function notifyResumeBlocked(ctx: ExtensionContext, result: Extract<AutoAdvanceResult, { kind: "blocked" }>): void {
+  const resumeCmd = s.stepMode ? "/gsd next" : "/gsd auto";
+  ctx.ui.notify(`Auto-mode blocked: ${result.reason}. Fix and run ${resumeCmd} to resume.`, "warning");
+  setLifecycleOutcome(ctx, {
+    status: "blocked",
+    title: "Auto-mode blocked",
+    detail: result.reason,
+    nextAction: `Fix the blocker, then run ${resumeCmd} to resume.`,
+    commands: ["/gsd status for overview", `${resumeCmd} to resume`, "/gsd doctor to diagnose"],
+  });
+}
+
 function ensureOrchestrationModule(ctx: ExtensionContext, pi: ExtensionAPI, basePath: string): void {
   s.orchestration = createWiredAutoOrchestrationModule(ctx, pi, basePath, lockBase());
 }
@@ -2317,7 +2435,7 @@ export async function startAuto(
     // This closes the journal gap reported in #3348 where the worker wrote side
     // effects (SUMMARY.md, DB updates) but died before emitting unit-end.
     emitCrashRecoveredUnitEnd(base, freshStartAssessment.lock);
-    clearLock(base);
+    clearStaleWorkerLock(base);
   }
 
   if (!s.paused) {
@@ -2388,6 +2506,8 @@ export async function startAuto(
     s.unitLifetimeDispatches.clear();
     if (!getLedger()) initMetrics(base);
     if (s.currentMilestoneId) setActiveMilestoneId(base, s.currentMilestoneId);
+    await openProjectDbIfPresent(base);
+    registerAutoWorkerForSession(s, base);
 
     // Re-register health level notification callback lost across process restart
     setLevelChangeCallback((_from, to, summary) => {
@@ -2495,7 +2615,12 @@ export async function startAuto(
     pi.events.emit(CMUX_CHANNELS.LOG, { preferences: loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, message: s.stepMode ? "Step-mode resumed." : "Auto-mode resumed.", level: "progress" });
 
     try {
-      await s.orchestration?.resume();
+      const resumeResult = await s.orchestration?.resume();
+      if (resumeResult?.kind === "blocked") {
+        notifyResumeBlocked(ctx, resumeResult);
+        await cleanupAfterLoopExit(ctx);
+        return;
+      }
     } catch (err) {
       debugLog("resume-orchestration-resume", { error: err instanceof Error ? err.message : String(err) });
     }
@@ -2516,6 +2641,7 @@ export async function startAuto(
   const bootstrapDeps: BootstrapDeps = {
     shouldUseWorktreeIsolation,
     registerSigtermHandler,
+    registerAutoWorkerForSession: (projectRoot) => registerAutoWorkerForSession(s, projectRoot),
     lockBase,
     buildLifecycle,
   };