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

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

@@ -15,6 +15,7 @@ import type {
 } from "@gsd/pi-coding-agent";
 import { deriveState } from "./state.js";
 import { loadFile, getManifestStatus } from "./files.js";
+import type { InterruptedSessionAssessment } from "./interrupted-session.js";
 import {
   loadEffectiveGSDPreferences,
   resolveSkillDiscoveryMode,
@@ -23,16 +24,9 @@ import {
 import { ensureGsdSymlink, isInheritedRepo, validateProjectId } from "./repo-identity.js";
 import { migrateToExternalState, recoverFailedMigration } from "./migrate-external.js";
 import { collectSecretsFromManifest } from "../get-secrets-from-user.js";
-import { gsdRoot, resolveMilestoneFile, milestonesDir } from "./paths.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,
@@ -248,6 +242,7 @@ export async function bootstrapAutoSession(
   verboseMode: boolean,
   requestedStepMode: boolean,
   deps: BootstrapDeps,
+  interrupted: InterruptedSessionAssessment,
 ): Promise<boolean> {
   const {
     shouldUseWorktreeIsolation,
@@ -361,51 +356,6 @@ export async function bootstrapAutoSession(
       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);
@@ -425,6 +375,10 @@ export async function bootstrapAutoSession(
       ctx.ui.notify(`Debug logging enabled → ${getDebugLogPath()}`, "info");
     }
 
+    if (interrupted.classification !== "recoverable") {
+      s.pendingCrashRecovery = null;
+    }
+
     // Invalidate caches before initial state derivation
     invalidateAllCaches();
 

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

@@ -1137,6 +1137,7 @@ function copyPlanningArtifacts(srcBase: string, wtPath: string): void {
   const srcGsd = join(srcBase, ".gsd");
   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"), {
@@ -1420,8 +1421,31 @@ export function mergeMilestoneToMain(
   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 /
@@ -1778,6 +1802,12 @@ export function mergeMilestoneToMain(
           }
         }
         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",
@@ -1975,23 +2005,38 @@ export function mergeMilestoneToMain(
   // 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: string | null = 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),
-      });
     }
   }
 
@@ -2020,4 +2065,3 @@ export function mergeMilestoneToMain(
 
   return { commitMessage, pushed, prCreated, codeFilesChanged };
 }
-

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

@@ -19,6 +19,11 @@ import type {
 import { deriveState } from "./state.js";
 import { parseUnitId } from "./unit-id.js";
 import type { GSDState } from "./types.js";
+import {
+  assessInterruptedSession,
+  readPausedSessionMetadata,
+  type InterruptedSessionAssessment,
+} from "./interrupted-session.js";
 import { getManifestStatus } from "./files.js";
 export { inlinePriorMilestoneSummary } from "./files.js";
 import { collectSecretsFromManifest } from "../get-secrets-from-user.js";
@@ -46,6 +51,7 @@ import {
   clearLock,
   readCrashLock,
   isLockProcessAlive,
+  formatCrashInfo,
 } from "./crash-recovery.js";
 import {
   acquireSessionLock,
@@ -118,6 +124,7 @@ import {
   formatTokenCount,
 } from "./metrics.js";
 import { setLogBasePath, logWarning, logError } 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";
@@ -920,6 +927,8 @@ export async function pauseAuto(
       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,
@@ -1141,7 +1150,10 @@ export async function startAuto(
   pi: ExtensionAPI,
   base: string,
   verboseMode: boolean,
-  options?: { step?: boolean },
+  options?: {
+    step?: boolean;
+    interrupted?: InterruptedSessionAssessment;
+  },
 ): Promise<void> {
   if (s.active) {
     debugLog("startAuto", { phase: "already-active", skipping: true });
@@ -1149,41 +1161,60 @@ export async function startAuto(
   }
 
   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); } 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
           );
-        } else if (meta.milestoneId) {
+        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 */
-            logWarning("session", `pause file cleanup failed: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
-          }
+            try { unlinkSync(pausedPath); } 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",
@@ -1192,22 +1223,54 @@ export async function startAuto(
             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;
+            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 ? ` (worktree)` : ""}.`,
+              `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" }); }
         }
       }
     } catch (err) {
       // 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) {
@@ -1232,26 +1295,19 @@ export async function startAuto(
     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 as any).newSession === "function") {
-      s.cmdCtx = ctx;
-    } else if (!s.cmdCtx) {
-      // No saved cmdCtx — this shouldn't happen, but handle gracefully
-      s.cmdCtx = ctx as ExtensionCommandContext;
-    }
-    // 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 as "info" | "warning" | "error");
+    });
+
     // ── Auto-worktree: re-enter worktree on resume ──
     if (
       s.currentMilestoneId &&
@@ -1275,6 +1331,11 @@ export async function startAuto(
       "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);
@@ -1305,8 +1366,8 @@ export async function startAuto(
       const activityDir = join(gsdRoot(s.basePath), "activity");
       const recovery = synthesizeCrashRecovery(
         s.basePath,
-        s.currentUnit?.type ?? "unknown",
-        s.currentUnit?.id ?? "unknown",
+        s.currentUnit?.type ?? s.pausedUnitType ?? "unknown",
+        s.currentUnit?.id ?? s.pausedUnitId ?? "unknown",
         s.pausedSessionFile ?? undefined,
         activityDir,
       );
@@ -1354,6 +1415,7 @@ export async function startAuto(
     verboseMode,
     requestedStepMode,
     bootstrapDeps,
+    freshStartAssessment,
   );
   if (!ready) return;
 
@@ -1467,27 +1529,6 @@ function ensurePreconditions(
   }
 }
 
-// ─── Diagnostics ──────────────────────────────────────────────────────────────
-
-/** Build recovery context from module state for recoverTimedOutUnit */
-function buildRecoveryContext(): import("./auto-timeout-recovery.js").RecoveryContext {
-  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: ExtensionContext,
   pi: ExtensionAPI,

package/src/resources/extensions/gsd/bootstrap/system-context.ts

@@ -168,7 +168,7 @@ export async function buildBeforeAgentStartResult(
   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}`;
@@ -481,7 +481,7 @@ function oneLine(text: string): string {
  * Check for an active forensics session and return the prompt content
  * so it can be re-injected on follow-up turns.
  */
-function buildForensicsContextInjection(basePath: string): string | null {
+export function buildForensicsContextInjection(basePath: string, prompt: string): string | null {
   const marker = readForensicsMarker(basePath);
   if (!marker) return null;
 
@@ -492,6 +492,12 @@ function buildForensicsContextInjection(basePath: string): string | null {
     return null;
   }
 
+  const trimmed = prompt.trim().toLowerCase().replace(/[.!?,]+$/g, "");
+  if (trimmed && !RESUME_INTENT_PATTERNS.test(trimmed)) {
+    clearForensicsMarker(basePath);
+    return null;
+  }
+
   return marker.promptContent;
 }
 

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

@@ -8,6 +8,7 @@ import { resolveMilestoneFile, resolveMilestonePath, resolveSliceFile, resolveSl
 import { deriveState, isMilestoneComplete } from "./state.js";
 import { invalidateAllCaches } from "./cache.js";
 import { loadEffectiveGSDPreferences, type GSDPreferences } from "./preferences.js";
+import { isClosedStatus } from "./status-guards.js";
 
 import type { DoctorIssue, DoctorIssueCode, DoctorReport } from "./doctor-types.js";
 import { GLOBAL_STATE_CODES } from "./doctor-types.js";
@@ -474,15 +475,16 @@ export async function runGSDDoctor(basePath: string, options?: { fix?: boolean;
     if (!roadmapContent) continue;
 
     // Normalize slices: prefer DB, fall back to parser
-    type NormSlice = RoadmapSliceEntry & { pending?: boolean };
+    type NormSlice = RoadmapSliceEntry & { pending?: boolean; skipped?: boolean };
     let slices: NormSlice[];
     if (isDbAvailable()) {
       const dbSlices = getMilestoneSlices(milestoneId);
       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") as RoadmapSliceEntry["risk"],
         depends: s.depends,
         demo: s.demo,
@@ -578,8 +580,9 @@ export async function runGSDDoctor(basePath: string, options?: { fix?: boolean;
       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) continue;
+        // 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({
           severity: slice.done ? "warning" : "error",
@@ -603,7 +606,8 @@ export async function runGSDDoctor(basePath: string, options?: { fix?: boolean;
       const tasksDir = resolveTasksDir(basePath, milestoneId, slice.id);
       if (!tasksDir) {
         // Pending slices haven't been planned yet — tasks/ is created on demand.
-        if (slice.pending) continue;
+        // Skipped slices may legitimately never create tasks/.
+        if (slice.pending || slice.skipped) continue;
         issues.push({
           severity: slice.done ? "warning" : "error",
           code: "missing_tasks_dir",

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

@@ -778,6 +778,7 @@ let currentDb: DbAdapter | null = null;
 let currentPath: string | null = null;
 let currentPid: number = 0;
 let _exitHandlerRegistered = false;
+let _dbOpenAttempted = false;
 
 export function getDbProvider(): ProviderName | null {
   loadProvider();
@@ -788,7 +789,18 @@ export function isDbAvailable(): boolean {
   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(): boolean {
+  return _dbOpenAttempted;
+}
+
 export function openDatabase(path: string): boolean {
+  _dbOpenAttempted = true;
   if (currentDb && currentPath !== path) closeDatabase();
   if (currentDb && currentPath === path) return true;