gsd-pi 2.67.0-dev.fe39184 → 2.68.0-dev.4cf2433

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

@@ -63,6 +63,8 @@ export class AutoSession {
     pendingVerificationRetry = null;
     verificationRetryCount = new Map();
     pausedSessionFile = null;
+    pausedUnitType = null;
+    pausedUnitId = null;
     resourceVersionOnStart = null;
     lastStateRebuildAt = 0;
     // ── Sidecar queue ─────────────────────────────────────────────────────
@@ -159,6 +161,8 @@ export class AutoSession {
         this.pendingVerificationRetry = null;
         this.verificationRetryCount.clear();
         this.pausedSessionFile = null;
+        this.pausedUnitType = null;
+        this.pausedUnitId = null;
         this.resourceVersionOnStart = null;
         this.lastStateRebuildAt = 0;
         // Metrics

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

@@ -104,7 +104,7 @@ export function isVerificationNotApplicable(value) {
     const v = (value ?? "").toLowerCase().trim().replace(/[.\s]+$/, "");
     if (!v || v === "none")
         return true;
-    return /^(?:none[\s._-]*(?:required|needed|planned)?|n\/?a|not[\s._-]+(?:applicable|required|needed|provided)|no[\s._-]+operational[\s\S]*)$/i.test(v);
+    return /^(?:none(?:[\s._\u2014-]+[\s\S]*)?|n\/?a|not[\s._-]+(?:applicable|required|needed|provided)|no[\s._-]+operational[\s\S]*)$/i.test(v);
 }
 // ─── Rules ────────────────────────────────────────────────────────────────
 export const DISPATCH_RULES = [

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

@@ -16,8 +16,7 @@ import { migrateToExternalState, recoverFailedMigration } from "./migrate-extern
 import { collectSecretsFromManifest } from "../get-secrets-from-user.js";
 import { gsdRoot, resolveMilestoneFile } from "./paths.js";
 import { invalidateAllCaches } from "./cache.js";
-import { synthesizeCrashRecovery } from "./session-forensics.js";
-import { writeLock, clearLock, readCrashLock, formatCrashInfo, isLockProcessAlive, } from "./crash-recovery.js";
+import { writeLock, clearLock } from "./crash-recovery.js";
 import { acquireSessionLock, releaseSessionLock, updateSessionLock, } from "./session-lock.js";
 import { ensureGitignore, untrackRuntimeFiles } from "./gitignore.js";
 import { nativeIsRepo, nativeInit, nativeAddAll, nativeCommit, nativeGetCurrentBranch, nativeDetectMainBranch, nativeCheckoutBranch, nativeBranchList, nativeBranchListMerged, nativeBranchDelete, nativeWorktreeRemove, } from "./native-git-bridge.js";
@@ -35,7 +34,6 @@ import { isDbAvailable, getMilestone, openDatabase } from "./gsd-db.js";
 import { hideFooter } from "./auto-dashboard.js";
 import { debugLog, enableDebug, isDebugEnabled, getDebugLogPath, } from "./debug-logger.js";
 import { logWarning, logError } from "./workflow-logger.js";
-import { parseUnitId } from "./unit-id.js";
 import { existsSync, mkdirSync, readdirSync, rmSync, statSync, unlinkSync, } from "node:fs";
 import { join } from "node:path";
 import { sep as pathSep } from "node:path";
@@ -174,7 +172,7 @@ export function auditOrphanedMilestoneBranches(basePath, isolationMode) {
     }
     return { recovered, warnings };
 }
-export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, requestedStepMode, deps) {
+export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, requestedStepMode, deps, interrupted) {
     const { shouldUseWorktreeIsolation, registerSigtermHandler, lockBase, buildResolver, } = deps;
     const lockResult = acquireSessionLock(base);
     if (!lockResult.acquired) {
@@ -264,33 +262,6 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
         }
         // Initialize GitServiceImpl
         s.gitService = new GitServiceImpl(s.basePath, loadEffectiveGSDPreferences()?.preferences?.git ?? {});
-        // Check for crash from previous session. Skip our own fresh bootstrap lock.
-        const crashLock = readCrashLock(base);
-        if (crashLock && crashLock.pid !== process.pid) {
-            if (isLockProcessAlive(crashLock)) {
-                ctx.ui.notify(`Another auto-mode session (PID ${crashLock.pid}) appears to be running.\nStop it with \`kill ${crashLock.pid}\` before starting a new session.`, "error");
-                return releaseLockAndReturn();
-            }
-            const recoveredMid = parseUnitId(crashLock.unitId).milestone;
-            const milestoneAlreadyComplete = recoveredMid
-                ? !!resolveMilestoneFile(base, recoveredMid, "SUMMARY")
-                : false;
-            if (milestoneAlreadyComplete) {
-                ctx.ui.notify(`Crash recovery: discarding stale context for ${crashLock.unitId} — milestone ${recoveredMid} is already complete.`, "info");
-            }
-            else {
-                const activityDir = join(gsdRoot(base), "activity");
-                const recovery = synthesizeCrashRecovery(base, crashLock.unitType, crashLock.unitId, crashLock.sessionFile, activityDir);
-                if (recovery && recovery.trace.toolCallCount > 0) {
-                    s.pendingCrashRecovery = recovery.prompt;
-                    ctx.ui.notify(`${formatCrashInfo(crashLock)}\nRecovered ${recovery.trace.toolCallCount} tool calls from crashed session. Resuming with full context.`, "warning");
-                }
-                else {
-                    ctx.ui.notify(`${formatCrashInfo(crashLock)}\nNo session data recovered. Resuming from disk state.`, "warning");
-                }
-            }
-            clearLock(base);
-        }
         // ── Debug mode ──
         if (!isDebugEnabled() && process.env.GSD_DEBUG === "1") {
             enableDebug(base);
@@ -308,6 +279,9 @@ export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, reques
             });
             ctx.ui.notify(`Debug logging enabled → ${getDebugLogPath()}`, "info");
         }
+        if (interrupted.classification !== "recoverable") {
+            s.pendingCrashRecovery = null;
+        }
         // Invalidate caches before initial state derivation
         invalidateAllCaches();
         // Clean stale runtime unit files for completed milestones (#887)

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

@@ -983,6 +983,8 @@ function copyPlanningArtifacts(srcBase, wtPath) {
     const dstGsd = join(wtPath, ".gsd");
     if (!existsSync(srcGsd))
         return;
+    if (isSamePath(srcGsd, dstGsd))
+        return;
     // Copy milestones/ directory (planning files, roadmaps, plans, research)
     safeCopyRecursive(join(srcGsd, "milestones"), join(dstGsd, "milestones"), {
         force: true,
@@ -1209,8 +1211,32 @@ function autoCommitDirtyState(cwd) {
 export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapContent) {
     const worktreeCwd = process.cwd();
     const milestoneBranch = autoWorktreeBranch(milestoneId);
-    // 1. Auto-commit dirty state in worktree before leaving
-    autoCommitDirtyState(worktreeCwd);
+    // 1. Auto-commit dirty state before leaving.
+    //    Guard: when we entered through an auto-worktree (originalBase is set),
+    //    only auto-commit when cwd is on the milestone branch. In parallel mode,
+    //    cwd may be on the integration branch after a prior merge's
+    //    MergeConflictError left cwd unrestored. Auto-committing on the
+    //    integration branch captures dirty files from OTHER milestones under a
+    //    misleading commit message, contaminating the main branch (#2929).
+    //
+    //    When originalBase is null (branch mode, no worktree), autoCommitDirtyState
+    //    runs unconditionally — the caller is responsible for cwd placement.
+    {
+        let shouldAutoCommit = true;
+        if (originalBase !== null) {
+            try {
+                const currentBranch = nativeGetCurrentBranch(worktreeCwd);
+                shouldAutoCommit = currentBranch === milestoneBranch;
+            }
+            catch {
+                // If we can't determine the branch, skip the auto-commit to be safe
+                shouldAutoCommit = false;
+            }
+        }
+        if (shouldAutoCommit) {
+            autoCommitDirtyState(worktreeCwd);
+        }
+    }
     // Reconcile worktree DB into main DB before leaving worktree context.
     // Skip when both paths resolve to the same physical file (shared WAL /
     // symlink layout) — ATTACHing a WAL-mode file to itself corrupts the
@@ -1551,6 +1577,12 @@ export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapCont
                     }
                 }
                 restoreShelter();
+                // Restore cwd so the caller is not stranded on the integration branch.
+                // Without this, the next mergeMilestoneToMain call in a parallel merge
+                // sequence uses process.cwd() (now the project root) as worktreeCwd,
+                // causing autoCommitDirtyState to commit unrelated milestone files to
+                // the integration branch (#2929).
+                process.chdir(previousCwd);
                 throw new MergeConflictError(codeConflicts, "squash", milestoneBranch, mainBranch);
             }
         }
@@ -1725,25 +1757,40 @@ export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapCont
     // changes (e.g. nativeHasChanges cache returned stale false, or auto-commit
     // silently failed), force one final commit so code is not destroyed by
     // `git worktree remove --force`.
+    //
+    // Guard: only run when worktreeCwd is on the milestone branch (#2929).
+    // In parallel mode or branch-mode merges, worktreeCwd may be the project
+    // root on the integration branch. Committing dirty state there would
+    // capture unrelated files from other milestones.
     if (existsSync(worktreeCwd)) {
+        let preTeardownBranch = null;
         try {
-            const dirtyCheck = nativeWorkingTreeStatus(worktreeCwd);
-            if (dirtyCheck) {
+            preTeardownBranch = nativeGetCurrentBranch(worktreeCwd);
+        }
+        catch (err) {
+            debugLog("mergeMilestoneToMain", { phase: "pre-teardown-branch-detect-failed", error: String(err) });
+        }
+        const isOnMilestoneBranch = preTeardownBranch === milestoneBranch;
+        if (isOnMilestoneBranch) {
+            try {
+                const dirtyCheck = nativeWorkingTreeStatus(worktreeCwd);
+                if (dirtyCheck) {
+                    debugLog("mergeMilestoneToMain", {
+                        phase: "pre-teardown-dirty",
+                        worktreeCwd,
+                        status: dirtyCheck.slice(0, 200),
+                    });
+                    nativeAddAllWithExclusions(worktreeCwd, RUNTIME_EXCLUSION_PATHS);
+                    nativeCommit(worktreeCwd, "chore: pre-teardown auto-commit of uncommitted worktree changes");
+                }
+            }
+            catch (e) {
                 debugLog("mergeMilestoneToMain", {
-                    phase: "pre-teardown-dirty",
-                    worktreeCwd,
-                    status: dirtyCheck.slice(0, 200),
+                    phase: "pre-teardown-commit-error",
+                    error: String(e),
                 });
-                nativeAddAllWithExclusions(worktreeCwd, RUNTIME_EXCLUSION_PATHS);
-                nativeCommit(worktreeCwd, "chore: pre-teardown auto-commit of uncommitted worktree changes");
             }
         }
-        catch (e) {
-            debugLog("mergeMilestoneToMain", {
-                phase: "pre-teardown-commit-error",
-                error: String(e),
-            });
-        }
     }
     // 12. Remove worktree directory first (must happen before branch deletion)
     try {

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

@@ -11,6 +11,7 @@
  */
 import { deriveState } from "./state.js";
 import { parseUnitId } from "./unit-id.js";
+import { assessInterruptedSession, readPausedSessionMetadata, } from "./interrupted-session.js";
 import { getManifestStatus } from "./files.js";
 export { inlinePriorMilestoneSummary } from "./files.js";
 import { collectSecretsFromManifest } from "../get-secrets-from-user.js";
@@ -18,7 +19,7 @@ import { gsdRoot, resolveMilestoneFile, resolveMilestonePath, resolveDir, milest
 import { invalidateAllCaches } from "./cache.js";
 import { clearActivityLogState } from "./activity-log.js";
 import { synthesizeCrashRecovery, getDeepDiagnostic, readActiveMilestoneId, } from "./session-forensics.js";
-import { writeLock, clearLock, readCrashLock, isLockProcessAlive, } from "./crash-recovery.js";
+import { writeLock, clearLock, readCrashLock, isLockProcessAlive, formatCrashInfo, } from "./crash-recovery.js";
 import { acquireSessionLock, getSessionLockStatus, releaseSessionLock, updateSessionLock, } from "./session-lock.js";
 import { resolveAutoSupervisorConfig, loadEffectiveGSDPreferences, getIsolationMode, } from "./preferences.js";
 import { sendDesktopNotification } from "./notifications.js";
@@ -34,7 +35,8 @@ import { clearSkillSnapshot } from "./skill-discovery.js";
 import { captureAvailableSkills, resetSkillTelemetry, } from "./skill-telemetry.js";
 import { getRtkSessionSavings } from "../shared/rtk-session-stats.js";
 import { initMetrics, resetMetrics, getLedger, getProjectTotals, formatCost, formatTokenCount, } from "./metrics.js";
-import { setLogBasePath, logWarning } from "./workflow-logger.js";
+import { logWarning } from "./workflow-logger.js";
+import { homedir } from "node:os";
 import { join } from "node:path";
 import { readFileSync, existsSync, mkdirSync, writeFileSync, unlinkSync } from "node:fs";
 import { atomicWriteSync } from "./atomic-write.js";
@@ -665,6 +667,8 @@ export async function pauseAuto(ctx, _pi, _errorContext) {
             stepMode: s.stepMode,
             pausedAt: new Date().toISOString(),
             sessionFile: s.pausedSessionFile,
+            unitType: s.currentUnit?.type ?? undefined,
+            unitId: s.currentUnit?.id ?? undefined,
             activeEngineId: s.activeEngineId,
             activeRunDir: s.activeRunDir,
             autoStartTime: s.autoStartTime,
@@ -853,38 +857,54 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         return;
     }
     const requestedStepMode = options?.step ?? false;
+    const interruptedAssessment = options?.interrupted ?? null;
     // Escape stale worktree cwd from a previous milestone (#608).
     base = escapeStaleWorktree(base);
+    const freshStartAssessment = interruptedAssessment
+        ?? await assessInterruptedSession(base);
+    if (freshStartAssessment.classification === "running") {
+        const pid = freshStartAssessment.lock?.pid;
+        ctx.ui.notify(pid
+            ? `Another auto-mode session (PID ${pid}) appears to be running.\nStop it with \`kill ${pid}\` before starting a new session.`
+            : "Another auto-mode session appears to be running.", "error");
+        return;
+    }
     // If resuming from paused state, just re-activate and dispatch next unit.
     // Check persisted paused-session first (#1383) — survives /exit.
     if (!s.paused) {
         try {
+            const meta = freshStartAssessment.pausedSession ?? readPausedSessionMetadata(base);
             const pausedPath = join(gsdRoot(base), "runtime", "paused-session.json");
-            if (existsSync(pausedPath)) {
-                const meta = JSON.parse(readFileSync(pausedPath, "utf-8"));
-                if (meta.activeEngineId && meta.activeEngineId !== "dev") {
-                    // Custom workflow resume — restore engine state
-                    s.activeEngineId = meta.activeEngineId;
-                    s.activeRunDir = meta.activeRunDir ?? null;
-                    s.originalBasePath = meta.originalBasePath || base;
-                    s.stepMode = meta.stepMode ?? requestedStepMode;
-                    s.autoStartTime = meta.autoStartTime || Date.now();
-                    s.paused = true;
-                    // Don't delete pause file yet — defer until lock is acquired.
-                    // If lock fails, the file must survive for retry.
-                    s.pausedSessionFile = pausedPath;
-                    ctx.ui.notify(`Resuming paused custom workflow${meta.activeRunDir ? ` (${meta.activeRunDir})` : ""}.`, "info");
+            if (meta?.activeEngineId && meta.activeEngineId !== "dev") {
+                // Custom workflow resume — restore engine state
+                s.activeEngineId = meta.activeEngineId;
+                s.activeRunDir = meta.activeRunDir ?? null;
+                s.originalBasePath = meta.originalBasePath || base;
+                s.stepMode = meta.stepMode ?? requestedStepMode;
+                s.autoStartTime = meta.autoStartTime || Date.now();
+                s.paused = true;
+                try {
+                    unlinkSync(pausedPath);
                 }
-                else if (meta.milestoneId) {
+                catch (e) {
+                    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");
+            }
+            else if (meta?.milestoneId) {
+                const shouldResumePausedSession = freshStartAssessment.classification === "recoverable"
+                    && (freshStartAssessment.hasResumableDiskState
+                        || !!freshStartAssessment.recoveryPrompt
+                        || !!freshStartAssessment.lock);
+                if (shouldResumePausedSession) {
                     // Validate the milestone still exists and isn't already complete (#1664).
                     const mDir = resolveMilestonePath(base, meta.milestoneId);
                     const summaryFile = resolveMilestoneFile(base, meta.milestoneId, "SUMMARY");
                     if (!mDir || summaryFile) {
-                        // Stale milestone — clean up and fall through to fresh bootstrap
                         try {
                             unlinkSync(pausedPath);
                         }
-                        catch (err) { /* non-fatal */
+                        catch (err) {
                             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");
@@ -893,12 +913,26 @@ 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.pausedUnitType = meta.unitType ?? null;
+                        s.pausedUnitId = meta.unitId ?? null;
                         s.autoStartTime = meta.autoStartTime || Date.now();
                         s.paused = true;
-                        // Don't delete pause file yet — defer until lock is acquired.
-                        // If lock fails, the file must survive for retry.
-                        s.pausedSessionFile = pausedPath;
-                        ctx.ui.notify(`Resuming paused session for ${meta.milestoneId}${meta.worktreePath ? ` (worktree)` : ""}.`, "info");
+                        try {
+                            unlinkSync(pausedPath);
+                        }
+                        catch (e) {
+                            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" });
                     }
                 }
             }
@@ -907,6 +941,30 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
             // Malformed or missing — proceed with fresh bootstrap
             logWarning("session", `paused-session restore failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
         }
+        // Guard against zero/missing autoStartTime after resume (#3585)
+        if (!s.autoStartTime || s.autoStartTime <= 0)
+            s.autoStartTime = Date.now();
+    }
+    if (!s.paused) {
+        s.stepMode = requestedStepMode;
+    }
+    if (freshStartAssessment.lock) {
+        clearLock(base);
+    }
+    if (!s.paused) {
+        s.pendingCrashRecovery =
+            freshStartAssessment.classification === "recoverable"
+                ? freshStartAssessment.recoveryPrompt
+                : null;
+        if (freshStartAssessment.classification === "recoverable" && freshStartAssessment.lock) {
+            const info = formatCrashInfo(freshStartAssessment.lock);
+            if (freshStartAssessment.recoveryToolCallCount > 0) {
+                ctx.ui.notify(`${info}\nRecovered ${freshStartAssessment.recoveryToolCallCount} tool calls from crashed session. Resuming with full context.`, "warning");
+            }
+            else if (freshStartAssessment.hasResumableDiskState) {
+                ctx.ui.notify(`${info}\nResuming from disk state.`, "warning");
+            }
+        }
     }
     if (s.paused) {
         const resumeLock = acquireSessionLock(base);
@@ -931,29 +989,19 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         s.active = true;
         s.verbose = verboseMode;
         s.stepMode = requestedStepMode;
-        // Preserve the original cmdCtx (ExtensionCommandContext with newSession)
-        // when resuming from a provider-error pause. The resume callback receives
-        // an ExtensionContext (from the agent_end hook) which lacks newSession —
-        // using it would crash runUnit with "newSession is not a function".
-        // Only override if the new ctx actually has newSession (user-initiated resume).
-        if ("newSession" in ctx && typeof ctx.newSession === "function") {
-            s.cmdCtx = ctx;
-        }
-        else if (!s.cmdCtx) {
-            // No saved cmdCtx — this shouldn't happen, but handle gracefully
-            s.cmdCtx = ctx;
-        }
-        // else: keep existing s.cmdCtx which has the real newSession
+        s.cmdCtx = ctx;
         s.basePath = base;
-        setLogBasePath(base);
-        if (!s.autoStartTime || s.autoStartTime <= 0)
-            s.autoStartTime = Date.now();
         s.unitDispatchCount.clear();
         s.unitLifetimeDispatches.clear();
         if (!getLedger())
             initMetrics(base);
         if (s.currentMilestoneId)
             setActiveMilestoneId(base, s.currentMilestoneId);
+        // Re-register health level notification callback lost across process restart
+        setLevelChangeCallback((_from, to, summary) => {
+            const level = to === "red" ? "error" : to === "yellow" ? "warning" : "info";
+            ctx.ui.notify(summary, level);
+        });
         // ── Auto-worktree: re-enter worktree on resume ──
         if (s.currentMilestoneId &&
             shouldUseWorktreeIsolation() &&
@@ -970,6 +1018,11 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         ctx.ui.setFooter(hideFooter);
         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
+        // bundled extension updates before resume-time verification/state logic runs.
+        const agentDir = process.env.GSD_CODING_AGENT_DIR || join(process.env.GSD_HOME || homedir(), ".gsd", "agent");
+        const { initResources } = await import("../../../" + "resource-loader.js");
+        initResources(agentDir);
         // Open the project DB before rebuild/derive so resume uses DB-backed
         // state instead of falling back to stale markdown parsing (#2940).
         await openProjectDbIfPresent(s.basePath);
@@ -996,7 +1049,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         invalidateAllCaches();
         if (s.pausedSessionFile) {
             const activityDir = join(gsdRoot(s.basePath), "activity");
-            const recovery = synthesizeCrashRecovery(s.basePath, s.currentUnit?.type ?? "unknown", s.currentUnit?.id ?? "unknown", s.pausedSessionFile ?? undefined, activityDir);
+            const recovery = synthesizeCrashRecovery(s.basePath, s.currentUnit?.type ?? s.pausedUnitType ?? "unknown", s.currentUnit?.id ?? s.pausedUnitId ?? "unknown", s.pausedSessionFile ?? undefined, activityDir);
             if (recovery && recovery.trace.toolCallCount > 0) {
                 s.pendingCrashRecovery = recovery.prompt;
                 ctx.ui.notify(`Recovered ${recovery.trace.toolCallCount} tool calls from paused session. Resuming with context.`, "info");
@@ -1018,7 +1071,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         lockBase,
         buildResolver,
     };
-    const ready = await bootstrapAutoSession(s, ctx, pi, base, verboseMode, requestedStepMode, bootstrapDeps);
+    const ready = await bootstrapAutoSession(s, ctx, pi, base, verboseMode, requestedStepMode, bootstrapDeps, freshStartAssessment);
     if (!ready)
         return;
     captureProjectRootEnv(s.originalBasePath || s.basePath);
@@ -1101,24 +1154,6 @@ function ensurePreconditions(unitType, unitId, base, state) {
         }
     }
 }
-// ─── Diagnostics ──────────────────────────────────────────────────────────────
-/** Build recovery context from module state for recoverTimedOutUnit */
-function buildRecoveryContext() {
-    return {
-        basePath: s.basePath,
-        verbose: s.verbose,
-        currentUnitStartedAt: s.currentUnit?.startedAt ?? Date.now(),
-        unitRecoveryCount: s.unitRecoveryCount,
-    };
-}
-/**
- * Test-only: expose skip-loop state for unit tests.
- * Not part of the public API.
- */
-/**
- * Dispatch a hook unit directly, bypassing normal pre-dispatch hooks.
- * Used for manual hook triggers via /gsd run-hook.
- */
 export async function dispatchHookUnit(ctx, pi, hookName, triggerUnitType, triggerUnitId, hookPrompt, hookModel, targetBasePath) {
     if (!s.active) {
         s.active = true;

package/dist/resources/extensions/gsd/bootstrap/system-context.js

@@ -141,7 +141,7 @@ export async function buildBeforeAgentStartResult(event, ctx) {
     warnDeprecatedAgentInstructions();
     const injection = await buildGuidedExecuteContextInjection(event.prompt, process.cwd());
     // Re-inject forensics context on follow-up turns (#2941)
-    const forensicsInjection = !injection ? buildForensicsContextInjection(process.cwd()) : null;
+    const forensicsInjection = !injection ? buildForensicsContextInjection(process.cwd(), event.prompt) : null;
     const worktreeBlock = buildWorktreeContextBlock();
     const fullSystem = `${event.systemPrompt}\n\n[SYSTEM CONTEXT — GSD]\n\n${systemContent}${preferenceBlock}${knowledgeBlock}${codebaseBlock}${memoryBlock}${newSkillsBlock}${worktreeBlock}`;
     stopContextTimer({
@@ -425,7 +425,7 @@ function oneLine(text) {
  * Check for an active forensics session and return the prompt content
  * so it can be re-injected on follow-up turns.
  */
-function buildForensicsContextInjection(basePath) {
+export function buildForensicsContextInjection(basePath, prompt) {
     const marker = readForensicsMarker(basePath);
     if (!marker)
         return null;
@@ -435,6 +435,11 @@ function buildForensicsContextInjection(basePath) {
         clearForensicsMarker(basePath);
         return null;
     }
+    const trimmed = prompt.trim().toLowerCase().replace(/[.!?,]+$/g, "");
+    if (trimmed && !RESUME_INTENT_PATTERNS.test(trimmed)) {
+        clearForensicsMarker(basePath);
+        return null;
+    }
     return marker.promptContent;
 }
 /**

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

@@ -7,6 +7,7 @@ import { resolveMilestoneFile, resolveMilestonePath, resolveSliceFile, resolveSl
 import { deriveState, isMilestoneComplete } from "./state.js";
 import { invalidateAllCaches } from "./cache.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
+import { isClosedStatus } from "./status-guards.js";
 import { GLOBAL_STATE_CODES } from "./doctor-types.js";
 import { checkGitHealth, checkRuntimeHealth, checkGlobalHealth, checkEngineHealth } from "./doctor-checks.js";
 import { checkEnvironmentHealth } from "./doctor-environment.js";
@@ -443,8 +444,9 @@ export async function runGSDDoctor(basePath, options) {
             slices = dbSlices.map(s => ({
                 id: s.id,
                 title: s.title,
-                done: s.status === "complete",
+                done: isClosedStatus(s.status),
                 pending: s.status === "pending",
+                skipped: s.status === "skipped",
                 risk: (s.risk || "medium"),
                 depends: s.depends,
                 demo: s.demo,
@@ -541,8 +543,9 @@ export async function runGSDDoctor(basePath, options) {
             const slicePath = resolveSlicePath(basePath, milestoneId, slice.id);
             if (!slicePath) {
                 // Pending slices haven't been planned yet — directories are created
-                // lazily by ensurePreconditions() at dispatch time. Skip them.
-                if (slice.pending)
+                // lazily by ensurePreconditions() at dispatch time. Skipped slices are
+                // intentionally allowed to remain summary-less and directory-less.
+                if (slice.pending || slice.skipped)
                     continue;
                 const expectedPath = relSlicePath(basePath, milestoneId, slice.id);
                 issues.push({
@@ -566,7 +569,8 @@ export async function runGSDDoctor(basePath, options) {
             const tasksDir = resolveTasksDir(basePath, milestoneId, slice.id);
             if (!tasksDir) {
                 // Pending slices haven't been planned yet — tasks/ is created on demand.
-                if (slice.pending)
+                // Skipped slices may legitimately never create tasks/.
+                if (slice.pending || slice.skipped)
                     continue;
                 issues.push({
                     severity: slice.done ? "warning" : "error",

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

@@ -701,6 +701,7 @@ let currentDb = null;
 let currentPath = null;
 let currentPid = 0;
 let _exitHandlerRegistered = false;
+let _dbOpenAttempted = false;
 export function getDbProvider() {
     loadProvider();
     return providerName;
@@ -708,7 +709,17 @@ export function getDbProvider() {
 export function isDbAvailable() {
     return currentDb !== null;
 }
+/**
+ * Returns true if openDatabase() has been called at least once this session.
+ * Used to distinguish "DB not yet initialized" from "DB genuinely unavailable"
+ * so that early callers (e.g. before_agent_start context injection) don't
+ * trigger a false degraded-mode warning.
+ */
+export function wasDbOpenAttempted() {
+    return _dbOpenAttempted;
+}
 export function openDatabase(path) {
+    _dbOpenAttempted = true;
     if (currentDb && currentPath !== path)
         closeDatabase();
     if (currentDb && currentPath === path)