gsd-pi 2.67.0-dev.5399650 → 2.67.0-dev.6fc2289

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/commands/catalog.ts

@@ -70,7 +70,7 @@ export const TOP_LEVEL_SUBCOMMANDS: readonly GsdCommandDefinition[] = [
   { cmd: "templates", desc: "List available workflow templates" },
   { cmd: "extensions", desc: "Manage extensions (list, enable, disable, info)" },
   { cmd: "fast", desc: "Toggle OpenAI service tier (on/off/flex/status)" },
-  { cmd: "mcp", desc: "MCP server status and connectivity check (status, check <server>)" },
+  { cmd: "mcp", desc: "MCP server status, connectivity, and local config bootstrap (status, check, init)" },
   { cmd: "rethink", desc: "Conversational project reorganization — reorder, park, discard, add milestones" },
   { cmd: "workflow", desc: "Custom workflow lifecycle (new, run, list, validate, pause, resume)" },
   { cmd: "codebase", desc: "Generate, refresh, and inspect the codebase map cache (.gsd/CODEBASE.md)" },
@@ -201,6 +201,7 @@ const NESTED_COMPLETIONS: CompletionMap = {
   mcp: [
     { cmd: "status", desc: "Show all MCP server statuses (default)" },
     { cmd: "check", desc: "Detailed status for a specific server" },
+    { cmd: "init", desc: "Write .mcp.json for the local GSD workflow MCP server" },
   ],
   doctor: [
     { cmd: "fix", desc: "Auto-fix detected issues" },

package/src/resources/extensions/gsd/commands/handlers/core.ts

@@ -60,7 +60,7 @@ export function showHelp(ctx: ExtensionCommandContext): void {
     "  /gsd hooks          Show post-unit hook configuration",
     "  /gsd extensions     Manage extensions  [list|enable|disable|info]",
     "  /gsd fast           Toggle OpenAI service tier  [on|off|flex|status]",
-    "  /gsd mcp            MCP server status and connectivity  [status|check <server>]",
+    "  /gsd mcp            MCP server status and connectivity  [status|check <server>|init [dir]]",
     "",
     "MAINTENANCE",
     "  /gsd doctor         Diagnose and repair .gsd/ state  [audit|fix|heal] [scope]",

package/src/resources/extensions/gsd/commands-mcp-status.ts

@@ -7,12 +7,15 @@
  *   /gsd mcp             — Overview of all servers (alias: /gsd mcp status)
  *   /gsd mcp status      — Same as bare /gsd mcp
  *   /gsd mcp check <srv> — Detailed status for a specific server
+ *   /gsd mcp init [dir]  — Write project-local GSD workflow MCP config
  */
 
 import type { ExtensionCommandContext } from "@gsd/pi-coding-agent";
 
 import { existsSync, readFileSync } from "node:fs";
-import { join } from "node:path";
+import { join, resolve } from "node:path";
+
+import { ensureProjectWorkflowMcpConfig } from "./mcp-project-config.js";
 
 // ─── Types ──────────────────────────────────────────────────────────────────
 
@@ -28,6 +31,28 @@ export interface McpServerDetail extends McpServerStatus {
   tools: string[];
 }
 
+export function formatMcpInitResult(
+  status: "created" | "updated" | "unchanged",
+  configPath: string,
+  targetPath: string,
+): string {
+  const summary =
+    status === "created"
+      ? "Created project MCP config."
+      : status === "updated"
+        ? "Updated project MCP config."
+        : "Project MCP config is already up to date.";
+
+  return [
+    summary,
+    "",
+    `Project: ${targetPath}`,
+    `Config:   ${configPath}`,
+    "",
+    "Claude Code can now load the GSD workflow MCP server from this folder.",
+  ].join("\n");
+}
+
 // ─── Config reader (standalone — does not import mcp-client internals) ──────
 
 interface McpServerRawConfig {
@@ -94,6 +119,7 @@ export function formatMcpStatusReport(servers: McpServerStatus[]): string {
       "No MCP servers configured.",
       "",
       "Add servers to .mcp.json or .gsd/mcp.json to enable MCP integrations.",
+      "Tip: run /gsd mcp init . to write the local GSD workflow MCP config.",
       "See: https://modelcontextprotocol.io/quickstart",
     ].join("\n");
   }
@@ -153,12 +179,31 @@ export async function handleMcpStatus(
   args: string,
   ctx: ExtensionCommandContext,
 ): Promise<void> {
-  const trimmed = args.trim().toLowerCase();
+  const trimmed = args.trim();
+  const lowered = trimmed.toLowerCase();
   const configs = readMcpConfigs();
 
+  // /gsd mcp init [dir]
+  if (!lowered || lowered === "status") {
+    // handled below
+  } else if (lowered === "init" || lowered.startsWith("init ")) {
+    const rawPath = trimmed.slice("init".length).trim();
+    const targetPath = resolve(rawPath || ".");
+    try {
+      const result = ensureProjectWorkflowMcpConfig(targetPath);
+      ctx.ui.notify(formatMcpInitResult(result.status, result.configPath, targetPath), "info");
+    } catch (err) {
+      ctx.ui.notify(
+        `Failed to prepare MCP config for ${targetPath}: ${err instanceof Error ? err.message : String(err)}`,
+        "error",
+      );
+    }
+    return;
+  }
+
   // /gsd mcp check <server>
-  if (trimmed.startsWith("check ")) {
-    const serverName = args.trim().slice("check ".length).trim();
+  if (lowered.startsWith("check ")) {
+    const serverName = trimmed.slice("check ".length).trim();
     const config = configs.find((c) => c.name === serverName);
     if (!config) {
       const available = configs.map((c) => c.name).join(", ") || "(none)";
@@ -202,7 +247,7 @@ export async function handleMcpStatus(
   }
 
   // /gsd mcp or /gsd mcp status
-  if (!trimmed || trimmed === "status") {
+  if (!lowered || lowered === "status") {
     // Build status for each server
     const statuses: McpServerStatus[] = [];
 
@@ -239,9 +284,10 @@ export async function handleMcpStatus(
 
   // Unknown subcommand
   ctx.ui.notify(
-    "Usage: /gsd mcp [status|check <server>]\n\n" +
+    "Usage: /gsd mcp [status|check <server>|init [dir]]\n\n" +
     "  status           Show all MCP server statuses (default)\n" +
-    "  check <server>   Detailed status for a specific server",
+    "  check <server>   Detailed status for a specific server\n" +
+    "  init [dir]       Write .mcp.json for the local GSD workflow MCP server",
     "warning",
   );
 }

package/src/resources/extensions/gsd/doctor-git-checks.ts

@@ -10,7 +10,7 @@ import { deriveState, isMilestoneComplete } from "./state.js";
 import { listWorktrees, resolveGitDir, worktreesDir } from "./worktree-manager.js";
 import { abortAndReset } from "./git-self-heal.js";
 import { RUNTIME_EXCLUSION_PATHS, resolveMilestoneIntegrationBranch, writeIntegrationBranch } from "./git-service.js";
-import { nativeIsRepo, nativeWorktreeList, nativeWorktreeRemove, nativeBranchList, nativeBranchDelete, nativeLsFiles, nativeRmCached, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddAllWithExclusions, nativeCommit } from "./native-git-bridge.js";
+import { nativeIsRepo, nativeWorktreeList, nativeWorktreeRemove, nativeBranchList, nativeBranchDelete, nativeLsFiles, nativeRmCached, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddTracked, nativeCommit } from "./native-git-bridge.js";
 import { getAllWorktreeHealth } from "./worktree-health.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 
@@ -386,19 +386,19 @@ export async function checkGitHealth(
             code: "stale_uncommitted_changes",
             scope: "project",
             unitId: "project",
-            message: `Uncommitted changes detected with no commit in ${mins} minute${mins === 1 ? "" : "s"} (threshold: ${thresholdMinutes}m). Snapshotting uncommitted changes.`,
+            message: `Uncommitted changes detected with no commit in ${mins} minute${mins === 1 ? "" : "s"} (threshold: ${thresholdMinutes}m). Snapshotting tracked files.`,
             fixable: true,
           });
 
           if (shouldFix("stale_uncommitted_changes")) {
             try {
-              nativeAddAllWithExclusions(basePath, RUNTIME_EXCLUSION_PATHS);
+              nativeAddTracked(basePath);
               const commitMsg = `gsd snapshot: uncommitted changes after ${mins}m inactivity`;
               const result = nativeCommit(basePath, commitMsg);
               if (result) {
                 fixesApplied.push(`created gsd snapshot after ${mins}m of uncommitted changes`);
               } else {
-                fixesApplied.push("gsd snapshot skipped — nothing to commit after staging changes");
+                fixesApplied.push("gsd snapshot skipped — nothing to commit after staging tracked files");
               }
             } catch {
               fixesApplied.push("failed to create gsd snapshot commit");

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

@@ -21,8 +21,8 @@ import { readCrashLock, isLockProcessAlive, clearLock } from "./crash-recovery.j
 import { abortAndReset } from "./git-self-heal.js";
 import { rebuildState } from "./doctor.js";
 import { deriveState } from "./state.js";
-import { RUNTIME_EXCLUSION_PATHS, resolveMilestoneIntegrationBranch } from "./git-service.js";
-import { nativeIsRepo, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddAllWithExclusions, nativeCommit } from "./native-git-bridge.js";
+import { resolveMilestoneIntegrationBranch } from "./git-service.js";
+import { nativeIsRepo, nativeHasChanges, nativeLastCommitEpoch, nativeGetCurrentBranch, nativeAddTracked, nativeCommit } from "./native-git-bridge.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 import { runEnvironmentChecks } from "./doctor-environment.js";
 
@@ -312,7 +312,7 @@ export async function preDispatchHealthGate(basePath: string): Promise<PreDispat
         if (minutesSinceCommit >= thresholdMinutes) {
           const mins = Math.floor(minutesSinceCommit);
           try {
-            nativeAddAllWithExclusions(basePath, RUNTIME_EXCLUSION_PATHS);
+            nativeAddTracked(basePath);
             const commitMsg = `gsd snapshot: pre-dispatch, uncommitted changes after ${mins}m inactivity`;
             const result = nativeCommit(basePath, commitMsg);
             if (result) {

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/guided-flow.ts

@@ -16,7 +16,12 @@ import { buildSkillActivationBlock } from "./auto-prompts.js";
 import { deriveState } from "./state.js";
 import { invalidateAllCaches } from "./cache.js";
 import { startAuto } from "./auto.js";
-import { readCrashLock, clearLock, formatCrashInfo } from "./crash-recovery.js";
+import { clearLock } from "./crash-recovery.js";
+import {
+  assessInterruptedSession,
+  formatInterruptedSessionRunningMessage,
+  formatInterruptedSessionSummary,
+} from "./interrupted-session.js";
 import { listUnitRuntimeRecords, clearUnitRuntimeRecord } from "./unit-runtime.js";
 import { resolveExpectedArtifactPath } from "./auto.js";
 import {
@@ -215,17 +220,9 @@ export function checkAutoStartAfterDiscuss(): boolean {
 
   // Gate 4: Discussion manifest process verification (multi-milestone only)
   // The LLM writes DISCUSSION-MANIFEST.json after each Phase 3 gate decision.
-  // If the project is multi-milestone, the manifest is required. When it is
-  // missing, fail closed instead of assuming the discussion finished.
+  // When it exists, validate it before auto-starting. Project history alone is
+  // not a reliable signal for the current discussion mode.
   const manifestPath = join(gsdRoot(basePath), "DISCUSSION-MANIFEST.json");
-  const requiresManifest = projectIds.length > 1 || findMilestoneIds(basePath).length > 1;
-  if (requiresManifest && !existsSync(manifestPath)) {
-    ctx.ui.notify(
-      "Multi-milestone discussion manifest is missing. Auto-start will remain paused until the manifest is written.",
-      "warning",
-    );
-    return false;
-  }
   if (existsSync(manifestPath)) {
     try {
       const manifest = JSON.parse(readFileSync(manifestPath, "utf-8"));
@@ -1322,36 +1319,45 @@ export async function showSmartEntry(
   // ── Self-heal stale runtime records from crashed auto-mode sessions ──
   selfHealRuntimeRecords(basePath, ctx);
 
-  // Check for crash from previous auto-mode session.
-  // Skip if the lock was written by the current process — acquireSessionLock()
-  // writes to the same file, so we'd always false-positive (#1398).
-  const crashLock = readCrashLock(basePath);
-  if (crashLock && crashLock.pid !== process.pid) {
-    clearLock(basePath);
+  const interrupted = await assessInterruptedSession(basePath);
+  if (interrupted.classification === "running") {
+    ctx.ui.notify(formatInterruptedSessionRunningMessage(interrupted), "error");
+    return;
+  }
 
-    // Bootstrap crash with zero completed units = no work was lost.
-    // Auto-discard instead of prompting the user — this commonly happens
-    // when the user exits during init wizard or discuss phase before any
-    // real auto-mode work begins.
-    const isBootstrapCrash = crashLock.unitType === "starting"
-      && crashLock.unitId === "bootstrap";
-
-    if (!isBootstrapCrash) {
-      const resume = await showNextAction(ctx, {
-        title: "GSD — Interrupted Session Detected",
-        summary: [formatCrashInfo(crashLock)],
-        actions: [
-          { id: "resume", label: "Resume with /gsd auto", description: "Pick up where it left off", recommended: true },
-          { id: "continue", label: "Continue manually", description: "Open the wizard as normal" },
-        ],
-      });
-      if (resume === "resume") {
-        await startAuto(ctx, pi, basePath, false);
-        return;
+  if (interrupted.classification === "stale") {
+    clearLock(basePath);
+    if (interrupted.pausedSession) {
+      try {
+        unlinkSync(join(gsdRoot(basePath), "runtime", "paused-session.json"));
+      } catch (e) {
+        logWarning("guided", `stale pause file cleanup failed: ${(e as Error).message}`, { file: "guided-flow.ts" });
       }
     }
+  } else if (interrupted.classification === "recoverable") {
+    if (interrupted.lock) clearLock(basePath);
+    const resumeLabel = interrupted.pausedSession?.stepMode
+      ? "Resume with /gsd next"
+      : "Resume with /gsd auto";
+    const resume = await showNextAction(ctx, {
+      title: "GSD — Interrupted Session Detected",
+      summary: formatInterruptedSessionSummary(interrupted),
+      actions: [
+        { id: "resume", label: resumeLabel, description: "Pick up where it left off", recommended: true },
+        { id: "continue", label: "Continue manually", description: "Open the wizard as normal" },
+      ],
+    });
+    if (resume === "resume") {
+      await startAuto(ctx, pi, basePath, false, {
+        interrupted,
+        step: interrupted.pausedSession?.stepMode ?? false,
+      });
+      return;
+    }
   }
 
+  // Always derive from the project root — the assessment may have derived
+  // state from a worktree path that was cleaned up in the stale branch above.
   const state = await deriveState(basePath);
 
   // Rebuild STATE.md from derived state before any dispatch (#3475).