gsd-pi 2.33.1-dev.ee47f1b → 2.34.0-dev.bbb5216

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

@@ -10,36 +10,30 @@
  */
 import { deriveState } from "./state.js";
 import { loadFile, getManifestStatus } from "./files.js";
-import { loadEffectiveGSDPreferences, resolveSkillDiscoveryMode, getIsolationMode } from "./preferences.js";
-import { isInsideWorktree, ensureGsdSymlink } from "./repo-identity.js";
-import { migrateToExternalState, recoverFailedMigration } from "./migrate-external.js";
-import { sendDesktopNotification } from "./notifications.js";
-import { sendRemoteNotification } from "../remote-questions/notify.js";
-import { gsdRoot, resolveMilestoneFile, } from "./paths.js";
+import { loadEffectiveGSDPreferences, resolveSkillDiscoveryMode, getIsolationMode, } from "./preferences.js";
+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 } from "./crash-recovery.js";
-import { acquireSessionLock, updateSessionLock, } from "./session-lock.js";
-import { selfHealRuntimeRecords } from "./auto-recovery.js";
+import { writeLock, clearLock, readCrashLock, formatCrashInfo, isLockProcessAlive, } from "./crash-recovery.js";
+import { acquireSessionLock, releaseSessionLock, updateSessionLock, } from "./session-lock.js";
 import { ensureGitignore, untrackRuntimeFiles } from "./gitignore.js";
-import { nativeIsRepo, nativeInit } from "./native-git-bridge.js";
-import { createGitService } from "./git-service.js";
+import { nativeIsRepo, nativeInit, nativeAddAll, nativeCommit, } from "./native-git-bridge.js";
+import { GitServiceImpl } from "./git-service.js";
 import { captureIntegrationBranch, detectWorktreeName, setActiveMilestoneId, } from "./worktree.js";
-import { createAutoWorktree, enterAutoWorktree, getAutoWorktreePath, } from "./auto-worktree.js";
-import { readResourceVersion } from "./resource-version.js";
+import { getAutoWorktreePath } from "./auto-worktree.js";
+import { readResourceVersion } from "./auto-worktree-sync.js";
 import { initMetrics } from "./metrics.js";
 import { initRoutingHistory } from "./routing-history.js";
 import { restoreHookState, resetHookState } from "./post-unit-hooks.js";
 import { resetProactiveHealing } from "./doctor-proactive.js";
 import { snapshotSkills } from "./skill-discovery.js";
 import { isDbAvailable } from "./gsd-db.js";
-import { loadPersistedKeys } from "./auto-recovery.js";
 import { hideFooter } from "./auto-dashboard.js";
-import { debugLog, enableDebug, isDebugEnabled, getDebugLogPath } from "./debug-logger.js";
-import { existsSync, mkdirSync, readdirSync, statSync, unlinkSync } from "node:fs";
+import { debugLog, enableDebug, isDebugEnabled, getDebugLogPath, } from "./debug-logger.js";
+import { existsSync, mkdirSync, readdirSync, statSync, unlinkSync, } from "node:fs";
 import { join } from "node:path";
-import { getErrorMessage } from "./error-utils.js";
-import { parseUnitId } from "./unit-id.js";
+import { sep as pathSep } from "node:path";
 /**
  * Bootstrap a fresh auto-mode session. Handles everything from git init
  * through secrets collection, returning when ready for the first
@@ -49,345 +43,372 @@ import { parseUnitId } from "./unit-id.js";
  * concurrent session detected). Returns true when ready to dispatch.
  */
 export async function bootstrapAutoSession(s, ctx, pi, base, verboseMode, requestedStepMode, deps) {
-    const { shouldUseWorktreeIsolation, registerSigtermHandler, lockBase } = deps;
-    // ── Session lock: acquire FIRST, before any state mutation ──────────────
-    // This is the primary guard against concurrent sessions on the same project.
-    // Uses OS-level file locking (proper-lockfile) to prevent TOCTOU races.
+    const { shouldUseWorktreeIsolation, registerSigtermHandler, lockBase, buildResolver, } = deps;
     const lockResult = acquireSessionLock(base);
     if (!lockResult.acquired) {
-        ctx.ui.notify(`${lockResult.reason}\nStop it with \`kill ${lockResult.existingPid ?? "the other process"}\` before starting a new session.`, "error");
+        ctx.ui.notify(lockResult.reason, "error");
         return false;
     }
-    // Ensure git repo exists
-    if (!nativeIsRepo(base)) {
-        const mainBranch = loadEffectiveGSDPreferences()?.preferences?.git?.main_branch || "main";
-        nativeInit(base, mainBranch);
-    }
-    // Ensure .gitignore has baseline patterns
-    const gitPrefs = loadEffectiveGSDPreferences()?.preferences?.git;
-    const manageGitignore = gitPrefs?.manage_gitignore;
-    ensureGitignore(base, { manageGitignore });
-    if (manageGitignore !== false)
-        untrackRuntimeFiles(base);
-    // Migrate legacy in-project .gsd/ to external state directory
-    recoverFailedMigration(base);
-    const migration = migrateToExternalState(base);
-    if (migration.error) {
-        ctx.ui.notify(`External state migration warning: ${migration.error}`, "warning");
-    }
-    // Ensure symlink exists (handles fresh projects and post-migration)
-    ensureGsdSymlink(base);
-    // Bootstrap .gsd/ if it doesn't exist
-    const gsdDir = gsdRoot(base);
-    if (!existsSync(gsdDir)) {
-        mkdirSync(join(gsdDir, "milestones"), { recursive: true });
+    function releaseLockAndReturn() {
+        releaseSessionLock(base);
+        clearLock(base);
+        return false;
     }
-    // Initialize GitServiceImpl
-    s.gitService = createGitService(s.basePath);
-    // Check for crash from previous session (use both old and new lock data).
-    // Skip if the lock PID matches this process — acquireSessionLock() writes
-    // to the same auto.lock file before this check, so we'd always false-positive.
-    const crashLock = readCrashLock(base);
-    if (crashLock && crashLock.pid !== process.pid) {
-        // We already hold the session lock, so no concurrent session is running.
-        // The crash lock is from a dead process — recover context from it.
-        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 ${recoveredMid} is already complete.`, "info");
+    try {
+        // Ensure git repo exists
+        if (!nativeIsRepo(base)) {
+            const mainBranch = loadEffectiveGSDPreferences()?.preferences?.git?.main_branch || "main";
+            nativeInit(base, mainBranch);
         }
-        else {
-            const activityDir = join(gsdRoot(base), "activity");
-            const recovery = synthesizeCrashRecovery(base, crashLock.unitType, crashLock.unitId, crashLock.sessionFile, activityDir);
-            if (recovery && recovery.trace.toolCallCount > 0) {
-                s.pendingCrashRecovery = recovery.prompt;
-                ctx.ui.notify(`${formatCrashInfo(crashLock)}\nRecovered ${recovery.trace.toolCallCount} tool calls from crashed session. Resuming with full context.`, "warning");
+        // Ensure .gitignore has baseline patterns
+        const gitPrefs = loadEffectiveGSDPreferences()?.preferences?.git;
+        const commitDocs = gitPrefs?.commit_docs;
+        const manageGitignore = gitPrefs?.manage_gitignore;
+        ensureGitignore(base, { commitDocs, manageGitignore });
+        if (manageGitignore !== false)
+            untrackRuntimeFiles(base);
+        // Bootstrap .gsd/ if it doesn't exist
+        const gsdDir = join(base, ".gsd");
+        if (!existsSync(gsdDir)) {
+            mkdirSync(join(gsdDir, "milestones"), { recursive: true });
+            if (commitDocs !== false) {
+                try {
+                    nativeAddAll(base);
+                    nativeCommit(base, "chore: init gsd");
+                }
+                catch {
+                    /* nothing to commit */
+                }
+            }
+        }
+        // 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 = crashLock.unitId.split("/")[0];
+            const milestoneAlreadyComplete = recoveredMid
+                ? !!resolveMilestoneFile(base, recoveredMid, "SUMMARY")
+                : false;
+            if (milestoneAlreadyComplete) {
+                ctx.ui.notify(`Crash recovery: discarding stale context for ${crashLock.unitId} — milestone ${recoveredMid} is already complete.`, "info");
             }
             else {
-                ctx.ui.notify(`${formatCrashInfo(crashLock)}\nNo session data recovered. Resuming from disk state.`, "warning");
+                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);
         }
-        clearLock(base);
-    }
-    // ── Debug mode ──
-    if (!isDebugEnabled() && process.env.GSD_DEBUG === "1") {
-        enableDebug(base);
-    }
-    if (isDebugEnabled()) {
-        const { isNativeParserAvailable } = await import("./native-parser-bridge.js");
-        debugLog("debug-start", {
-            platform: process.platform,
-            arch: process.arch,
-            node: process.version,
-            model: ctx.model?.id ?? "unknown",
-            provider: ctx.model?.provider ?? "unknown",
-            nativeParser: isNativeParserAvailable(),
-            cwd: base,
-        });
-        ctx.ui.notify(`Debug logging enabled → ${getDebugLogPath()}`, "info");
-    }
-    // Invalidate caches before initial state derivation
-    invalidateAllCaches();
-    // Clean stale runtime unit files for completed milestones (#887)
-    try {
-        const runtimeUnitsDir = join(gsdRoot(base), "runtime", "units");
-        if (existsSync(runtimeUnitsDir)) {
-            for (const file of readdirSync(runtimeUnitsDir)) {
-                if (!file.endsWith(".json"))
-                    continue;
-                const midMatch = file.match(/(M\d+(?:-[a-z0-9]{6})?)/);
-                if (!midMatch)
-                    continue;
-                const mid = midMatch[1];
-                if (resolveMilestoneFile(base, mid, "SUMMARY")) {
-                    try {
-                        unlinkSync(join(runtimeUnitsDir, file));
-                    }
-                    catch (e) {
-                        debugLog("stale-unit-cleanup-failed", { file, error: getErrorMessage(e) });
+        // ── Debug mode ──
+        if (!isDebugEnabled() && process.env.GSD_DEBUG === "1") {
+            enableDebug(base);
+        }
+        if (isDebugEnabled()) {
+            const { isNativeParserAvailable } = await import("./native-parser-bridge.js");
+            debugLog("debug-start", {
+                platform: process.platform,
+                arch: process.arch,
+                node: process.version,
+                model: ctx.model?.id ?? "unknown",
+                provider: ctx.model?.provider ?? "unknown",
+                nativeParser: isNativeParserAvailable(),
+                cwd: base,
+            });
+            ctx.ui.notify(`Debug logging enabled → ${getDebugLogPath()}`, "info");
+        }
+        // Invalidate caches before initial state derivation
+        invalidateAllCaches();
+        // Clean stale runtime unit files for completed milestones (#887)
+        try {
+            const runtimeUnitsDir = join(gsdRoot(base), "runtime", "units");
+            if (existsSync(runtimeUnitsDir)) {
+                for (const file of readdirSync(runtimeUnitsDir)) {
+                    if (!file.endsWith(".json"))
+                        continue;
+                    const midMatch = file.match(/(M\d+(?:-[a-z0-9]{6})?)/);
+                    if (!midMatch)
+                        continue;
+                    const mid = midMatch[1];
+                    if (resolveMilestoneFile(base, mid, "SUMMARY")) {
+                        try {
+                            unlinkSync(join(runtimeUnitsDir, file));
+                        }
+                        catch (e) {
+                            debugLog("stale-unit-cleanup-failed", {
+                                file,
+                                error: e instanceof Error ? e.message : String(e),
+                            });
+                        }
                     }
                 }
             }
         }
-    }
-    catch (e) {
-        debugLog("stale-unit-dir-cleanup-failed", { error: getErrorMessage(e) });
-    }
-    let state = await deriveState(base);
-    // Milestone branch recovery (#601)
-    let hasSurvivorBranch = false;
-    if (state.activeMilestone &&
-        (state.phase === "pre-planning" || state.phase === "needs-discussion") &&
-        shouldUseWorktreeIsolation() &&
-        !detectWorktreeName(base) &&
-        !isInsideWorktree(base)) {
-        const milestoneBranch = `milestone/${state.activeMilestone.id}`;
-        const { nativeBranchExists } = await import("./native-git-bridge.js");
-        hasSurvivorBranch = nativeBranchExists(base, milestoneBranch);
-        if (hasSurvivorBranch) {
-            ctx.ui.notify(`Found prior session branch ${milestoneBranch}. Resuming.`, "info");
+        catch (e) {
+            debugLog("stale-unit-dir-cleanup-failed", {
+                error: e instanceof Error ? e.message : String(e),
+            });
         }
-    }
-    if (!hasSurvivorBranch) {
-        // No active work — start a new milestone via discuss flow
-        if (!state.activeMilestone || state.phase === "complete") {
-            const { showSmartEntry } = await import("./guided-flow.js");
-            await showSmartEntry(ctx, pi, base, { step: requestedStepMode });
-            invalidateAllCaches();
-            const postState = await deriveState(base);
-            if (postState.activeMilestone && postState.phase !== "complete" && postState.phase !== "pre-planning") {
-                state = postState;
+        let state = await deriveState(base);
+        // Stale worktree state recovery (#654)
+        if (state.activeMilestone &&
+            shouldUseWorktreeIsolation() &&
+            !detectWorktreeName(base)) {
+            const wtPath = getAutoWorktreePath(base, state.activeMilestone.id);
+            if (wtPath) {
+                state = await deriveState(wtPath);
             }
-            else if (postState.activeMilestone && postState.phase === "pre-planning") {
-                const contextFile = resolveMilestoneFile(base, postState.activeMilestone.id, "CONTEXT");
-                const hasContext = !!(contextFile && await loadFile(contextFile));
-                if (hasContext) {
-                    state = postState;
-                }
-                else {
-                    ctx.ui.notify("Discussion completed but no milestone context was written. Run /gsd to try the discussion again, or /gsd auto after creating the milestone manually.", "warning");
-                    return false;
-                }
-            }
-            else {
-                return false;
+        }
+        // Milestone branch recovery (#601)
+        let hasSurvivorBranch = false;
+        if (state.activeMilestone &&
+            (state.phase === "pre-planning" || state.phase === "needs-discussion") &&
+            shouldUseWorktreeIsolation() &&
+            !detectWorktreeName(base) &&
+            !base.includes(`${pathSep}.gsd${pathSep}worktrees${pathSep}`)) {
+            const milestoneBranch = `milestone/${state.activeMilestone.id}`;
+            const { nativeBranchExists } = await import("./native-git-bridge.js");
+            hasSurvivorBranch = nativeBranchExists(base, milestoneBranch);
+            if (hasSurvivorBranch) {
+                ctx.ui.notify(`Found prior session branch ${milestoneBranch}. Resuming.`, "info");
             }
         }
-        // Active milestone exists but has no roadmap
-        if (state.phase === "pre-planning") {
-            const mid = state.activeMilestone.id;
-            const contextFile = resolveMilestoneFile(base, mid, "CONTEXT");
-            const hasContext = !!(contextFile && await loadFile(contextFile));
-            if (!hasContext) {
+        if (!hasSurvivorBranch) {
+            // No active work — start a new milestone via discuss flow
+            if (!state.activeMilestone || state.phase === "complete") {
                 const { showSmartEntry } = await import("./guided-flow.js");
                 await showSmartEntry(ctx, pi, base, { step: requestedStepMode });
                 invalidateAllCaches();
                 const postState = await deriveState(base);
-                if (postState.activeMilestone && postState.phase !== "pre-planning") {
+                if (postState.activeMilestone &&
+                    postState.phase !== "complete" &&
+                    postState.phase !== "pre-planning") {
                     state = postState;
                 }
+                else if (postState.activeMilestone &&
+                    postState.phase === "pre-planning") {
+                    const contextFile = resolveMilestoneFile(base, postState.activeMilestone.id, "CONTEXT");
+                    const hasContext = !!(contextFile && (await loadFile(contextFile)));
+                    if (hasContext) {
+                        state = postState;
+                    }
+                    else {
+                        ctx.ui.notify("Discussion completed but no milestone context was written. Run /gsd to try the discussion again, or /gsd auto after creating the milestone manually.", "warning");
+                        return releaseLockAndReturn();
+                    }
+                }
                 else {
-                    ctx.ui.notify("Discussion completed but milestone context is still missing. Run /gsd to try again.", "warning");
-                    return false;
+                    return releaseLockAndReturn();
+                }
+            }
+            // Active milestone exists but has no roadmap
+            if (state.phase === "pre-planning") {
+                const mid = state.activeMilestone.id;
+                const contextFile = resolveMilestoneFile(base, mid, "CONTEXT");
+                const hasContext = !!(contextFile && (await loadFile(contextFile)));
+                if (!hasContext) {
+                    const { showSmartEntry } = await import("./guided-flow.js");
+                    await showSmartEntry(ctx, pi, base, { step: requestedStepMode });
+                    invalidateAllCaches();
+                    const postState = await deriveState(base);
+                    if (postState.activeMilestone && postState.phase !== "pre-planning") {
+                        state = postState;
+                    }
+                    else {
+                        ctx.ui.notify("Discussion completed but milestone context is still missing. Run /gsd to try again.", "warning");
+                        return releaseLockAndReturn();
+                    }
                 }
             }
         }
-    }
-    // Unreachable safety check
-    if (!state.activeMilestone) {
-        const { showSmartEntry } = await import("./guided-flow.js");
-        await showSmartEntry(ctx, pi, base, { step: requestedStepMode });
-        return false;
-    }
-    // ── Initialize session state ──
-    s.active = true;
-    s.stepMode = requestedStepMode;
-    s.verbose = verboseMode;
-    s.cmdCtx = ctx;
-    s.basePath = base;
-    s.unitDispatchCount.clear();
-    s.unitRecoveryCount.clear();
-    s.unitConsecutiveSkips.clear();
-    s.lastBudgetAlertLevel = 0;
-    s.unitLifetimeDispatches.clear();
-    s.completedKeySet.clear();
-    loadPersistedKeys(base, s.completedKeySet);
-    resetHookState();
-    restoreHookState(base);
-    resetProactiveHealing();
-    s.autoStartTime = Date.now();
-    s.resourceVersionOnStart = readResourceVersion();
-    s.completedUnits = [];
-    s.pendingQuickTasks = [];
-    s.currentUnit = null;
-    s.currentMilestoneId = state.activeMilestone?.id ?? null;
-    s.originalModelId = ctx.model?.id ?? null;
-    s.originalModelProvider = ctx.model?.provider ?? null;
-    // Register SIGTERM handler
-    registerSigtermHandler(base);
-    // Capture integration branch
-    if (s.currentMilestoneId) {
-        if (getIsolationMode() !== "none") {
-            captureIntegrationBranch(base, s.currentMilestoneId);
+        // Unreachable safety check
+        if (!state.activeMilestone) {
+            const { showSmartEntry } = await import("./guided-flow.js");
+            await showSmartEntry(ctx, pi, base, { step: requestedStepMode });
+            return releaseLockAndReturn();
         }
-        setActiveMilestoneId(base, s.currentMilestoneId);
-    }
-    // ── Auto-worktree setup ──
-    s.originalBasePath = base;
-    if (s.currentMilestoneId && shouldUseWorktreeIsolation() && !detectWorktreeName(base) && !isInsideWorktree(base)) {
-        try {
-            const existingWtPath = getAutoWorktreePath(base, s.currentMilestoneId);
-            if (existingWtPath) {
-                const wtPath = enterAutoWorktree(base, s.currentMilestoneId);
-                s.basePath = wtPath;
-                s.gitService = createGitService(s.basePath);
-                ctx.ui.notify(`Entered auto-worktree at ${wtPath}`, "info");
+        // ── Initialize session state ──
+        s.active = true;
+        s.stepMode = requestedStepMode;
+        s.verbose = verboseMode;
+        s.cmdCtx = ctx;
+        s.basePath = base;
+        s.unitDispatchCount.clear();
+        s.unitRecoveryCount.clear();
+        s.lastBudgetAlertLevel = 0;
+        s.unitLifetimeDispatches.clear();
+        resetHookState();
+        restoreHookState(base);
+        resetProactiveHealing();
+        s.autoStartTime = Date.now();
+        s.resourceVersionOnStart = readResourceVersion();
+        s.completedUnits = [];
+        s.pendingQuickTasks = [];
+        s.currentUnit = null;
+        s.currentMilestoneId = state.activeMilestone?.id ?? null;
+        s.originalModelId = ctx.model?.id ?? null;
+        s.originalModelProvider = ctx.model?.provider ?? null;
+        // Register SIGTERM handler
+        registerSigtermHandler(base);
+        // Capture integration branch
+        if (s.currentMilestoneId) {
+            if (getIsolationMode() !== "none") {
+                captureIntegrationBranch(base, s.currentMilestoneId, { commitDocs });
             }
-            else {
-                const wtPath = createAutoWorktree(base, s.currentMilestoneId);
-                s.basePath = wtPath;
-                s.gitService = createGitService(s.basePath);
-                ctx.ui.notify(`Created auto-worktree at ${wtPath}`, "info");
+            setActiveMilestoneId(base, s.currentMilestoneId);
+        }
+        // ── Auto-worktree setup ──
+        s.originalBasePath = base;
+        const isUnderGsdWorktrees = (p) => {
+            const marker = `${pathSep}.gsd${pathSep}worktrees${pathSep}`;
+            if (p.includes(marker))
+                return true;
+            const worktreesSuffix = `${pathSep}.gsd${pathSep}worktrees`;
+            return p.endsWith(worktreesSuffix);
+        };
+        if (s.currentMilestoneId &&
+            shouldUseWorktreeIsolation() &&
+            !detectWorktreeName(base) &&
+            !isUnderGsdWorktrees(base)) {
+            buildResolver().enterMilestone(s.currentMilestoneId, {
+                notify: ctx.ui.notify.bind(ctx.ui),
+            });
+            if (s.basePath !== base) {
+                // Successfully entered worktree — re-register SIGTERM handler at original base
+                registerSigtermHandler(s.originalBasePath);
             }
-            registerSigtermHandler(s.originalBasePath);
         }
-        catch (err) {
-            ctx.ui.notify(`Auto-worktree setup failed: ${getErrorMessage(err)}. Continuing in project root.`, "warning");
+        // ── DB lifecycle ──
+        const gsdDbPath = join(s.basePath, ".gsd", "gsd.db");
+        const gsdDirPath = join(s.basePath, ".gsd");
+        if (existsSync(gsdDirPath) && !existsSync(gsdDbPath)) {
+            const hasDecisions = existsSync(join(gsdDirPath, "DECISIONS.md"));
+            const hasRequirements = existsSync(join(gsdDirPath, "REQUIREMENTS.md"));
+            const hasMilestones = existsSync(join(gsdDirPath, "milestones"));
+            if (hasDecisions || hasRequirements || hasMilestones) {
+                try {
+                    const { openDatabase: openDb } = await import("./gsd-db.js");
+                    const { migrateFromMarkdown } = await import("./md-importer.js");
+                    openDb(gsdDbPath);
+                    migrateFromMarkdown(s.basePath);
+                }
+                catch (err) {
+                    process.stderr.write(`gsd-migrate: auto-migration failed: ${err.message}\n`);
+                }
+            }
         }
-    }
-    // ── DB lifecycle ──
-    const gsdDbPath = join(gsdRoot(s.basePath), "gsd.db");
-    const gsdDirPath = gsdRoot(s.basePath);
-    if (existsSync(gsdDirPath) && !existsSync(gsdDbPath)) {
-        const hasDecisions = existsSync(join(gsdDirPath, "DECISIONS.md"));
-        const hasRequirements = existsSync(join(gsdDirPath, "REQUIREMENTS.md"));
-        const hasMilestones = existsSync(join(gsdDirPath, "milestones"));
-        if (hasDecisions || hasRequirements || hasMilestones) {
+        if (existsSync(gsdDbPath) && !isDbAvailable()) {
             try {
                 const { openDatabase: openDb } = await import("./gsd-db.js");
-                const { migrateFromMarkdown } = await import("./md-importer.js");
                 openDb(gsdDbPath);
-                migrateFromMarkdown(s.basePath);
             }
             catch (err) {
-                process.stderr.write(`gsd-migrate: auto-migration failed: ${err.message}\n`);
+                process.stderr.write(`gsd-db: failed to open existing database: ${err.message}\n`);
             }
         }
-    }
-    if (existsSync(gsdDbPath) && !isDbAvailable()) {
+        // Initialize metrics
+        initMetrics(s.basePath);
+        // Initialize routing history
+        initRoutingHistory(s.basePath);
+        // Capture session's model at auto-mode start (#650)
+        const currentModel = ctx.model;
+        if (currentModel) {
+            s.autoModeStartModel = {
+                provider: currentModel.provider,
+                id: currentModel.id,
+            };
+        }
+        // Snapshot installed skills
+        if (resolveSkillDiscoveryMode() !== "off") {
+            snapshotSkills();
+        }
+        ctx.ui.setStatus("gsd-auto", s.stepMode ? "next" : "auto");
+        ctx.ui.setFooter(hideFooter);
+        const modeLabel = s.stepMode ? "Step-mode" : "Auto-mode";
+        const pendingCount = (state.registry ?? []).filter((m) => m.status !== "complete" && m.status !== "parked").length;
+        const scopeMsg = pendingCount > 1
+            ? `Will loop through ${pendingCount} milestones.`
+            : "Will loop until milestone complete.";
+        ctx.ui.notify(`${modeLabel} started. ${scopeMsg}`, "info");
+        updateSessionLock(lockBase(), "starting", s.currentMilestoneId ?? "unknown", 0);
+        writeLock(lockBase(), "starting", s.currentMilestoneId ?? "unknown", 0);
+        // Secrets collection gate
+        const mid = state.activeMilestone.id;
         try {
-            const { openDatabase: openDb } = await import("./gsd-db.js");
-            openDb(gsdDbPath);
+            const manifestStatus = await getManifestStatus(base, mid);
+            if (manifestStatus && manifestStatus.pending.length > 0) {
+                const result = await collectSecretsFromManifest(base, mid, ctx);
+                if (result &&
+                    result.applied &&
+                    result.skipped &&
+                    result.existingSkipped) {
+                    ctx.ui.notify(`Secrets collected: ${result.applied.length} applied, ${result.skipped.length} skipped, ${result.existingSkipped.length} already set.`, "info");
+                }
+                else {
+                    ctx.ui.notify("Secrets collection skipped.", "info");
+                }
+            }
         }
         catch (err) {
-            process.stderr.write(`gsd-db: failed to open existing database: ${err.message}\n`);
-        }
-    }
-    // Initialize metrics
-    initMetrics(s.basePath);
-    // Initialize routing history
-    initRoutingHistory(s.basePath);
-    // Capture session's model at auto-mode start (#650)
-    const currentModel = ctx.model;
-    if (currentModel) {
-        s.autoModeStartModel = { provider: currentModel.provider, id: currentModel.id };
-    }
-    // Snapshot installed skills
-    if (resolveSkillDiscoveryMode() !== "off") {
-        snapshotSkills();
-    }
-    ctx.ui.setStatus("gsd-auto", s.stepMode ? "next" : "auto");
-    ctx.ui.setFooter(hideFooter);
-    const modeLabel = s.stepMode ? "Step-mode" : "Auto-mode";
-    const pendingCount = (state.registry ?? []).filter(m => m.status !== 'complete' && m.status !== 'parked').length;
-    const scopeMsg = pendingCount > 1
-        ? `Will loop through ${pendingCount} milestones.`
-        : "Will loop until milestone complete.";
-    ctx.ui.notify(`${modeLabel} started. ${scopeMsg}`, "info");
-    // Update lock file with milestone info (OS lock already acquired at bootstrap start)
-    updateSessionLock(lockBase(), "starting", s.currentMilestoneId ?? "unknown", 0);
-    writeLock(lockBase(), "starting", s.currentMilestoneId ?? "unknown", 0);
-    // Secrets collection gate — pause instead of blocking (#1146)
-    const mid = state.activeMilestone.id;
-    try {
-        const manifestStatus = await getManifestStatus(base, mid);
-        if (manifestStatus && manifestStatus.pending.length > 0) {
-            const pendingKeys = manifestStatus.pending;
-            const keyList = pendingKeys.map((k) => `  • ${k}`).join("\n");
-            s.paused = true;
-            s.pausedForSecrets = true;
-            ctx.ui.notify(`Auto-mode paused: ${pendingKeys.length} env variable${pendingKeys.length > 1 ? "s" : ""} needed for ${mid}.\n${keyList}\n\nCollect them with /gsd secrets, then resume with /gsd auto.`, "warning");
-            ctx.ui.setStatus("gsd-auto", "paused");
-            sendDesktopNotification("GSD — Secrets Required", `${pendingKeys.length} env variable(s) needed for ${mid}. Run /gsd secrets to provide them.`, "warning", "attention");
-            // Notify remote channel if configured (one-way — never collect secrets via remote)
-            sendRemoteNotification("GSD — Secrets Required", `Auto-mode paused: ${pendingKeys.length} env variable(s) needed for ${mid}.\n${keyList}\n\nReturn to the terminal and run /gsd secrets to provide them securely.`).catch(() => { }); // fire-and-forget
-            return false;
+            ctx.ui.notify(`Secrets collection error: ${err instanceof Error ? err.message : String(err)}. Continuing with next task.`, "warning");
         }
-    }
-    catch (err) {
-        ctx.ui.notify(`Secrets check error: ${getErrorMessage(err)}. Continuing without secrets.`, "warning");
-    }
-    // Self-heal: clear stale runtime records
-    await selfHealRuntimeRecords(s.basePath, ctx, s.completedKeySet);
-    // Self-heal: remove stale .git/index.lock
-    try {
-        const gitLockFile = join(base, ".git", "index.lock");
-        if (existsSync(gitLockFile)) {
-            const lockAge = Date.now() - statSync(gitLockFile).mtimeMs;
-            if (lockAge > 60_000) {
-                unlinkSync(gitLockFile);
-                ctx.ui.notify("Removed stale .git/index.lock from prior crash.", "info");
+        // Self-heal: remove stale .git/index.lock
+        try {
+            const gitLockFile = join(base, ".git", "index.lock");
+            if (existsSync(gitLockFile)) {
+                const lockAge = Date.now() - statSync(gitLockFile).mtimeMs;
+                if (lockAge > 60_000) {
+                    unlinkSync(gitLockFile);
+                    ctx.ui.notify("Removed stale .git/index.lock from prior crash.", "info");
+                }
             }
         }
-    }
-    catch (e) {
-        debugLog("git-lock-cleanup-failed", { error: getErrorMessage(e) });
-    }
-    // Pre-flight: validate milestone queue
-    try {
-        const msDir = join(gsdRoot(base), "milestones");
-        if (existsSync(msDir)) {
-            const milestoneIds = readdirSync(msDir, { withFileTypes: true })
-                .filter(d => d.isDirectory() && /^M\d{3}/.test(d.name))
-                .map(d => d.name.match(/^(M\d{3})/)?.[1] ?? d.name);
-            if (milestoneIds.length > 1) {
-                const issues = [];
-                for (const id of milestoneIds) {
-                    const draft = resolveMilestoneFile(base, id, "CONTEXT-DRAFT");
-                    if (draft)
-                        issues.push(`${id}: has CONTEXT-DRAFT.md (will pause for discussion)`);
-                }
-                if (issues.length > 0) {
-                    ctx.ui.notify(`Pre-flight: ${milestoneIds.length} milestones queued.\n${issues.map(i => `  ⚠ ${i}`).join("\n")}`, "warning");
-                }
-                else {
-                    ctx.ui.notify(`Pre-flight: ${milestoneIds.length} milestones queued. All have full context.`, "info");
+        catch (e) {
+            debugLog("git-lock-cleanup-failed", {
+                error: e instanceof Error ? e.message : String(e),
+            });
+        }
+        // Pre-flight: validate milestone queue
+        try {
+            const msDir = join(base, ".gsd", "milestones");
+            if (existsSync(msDir)) {
+                const milestoneIds = readdirSync(msDir, { withFileTypes: true })
+                    .filter((d) => d.isDirectory() && /^M\d{3}/.test(d.name))
+                    .map((d) => d.name.match(/^(M\d{3})/)?.[1] ?? d.name);
+                if (milestoneIds.length > 1) {
+                    const issues = [];
+                    for (const id of milestoneIds) {
+                        const draft = resolveMilestoneFile(base, id, "CONTEXT-DRAFT");
+                        if (draft)
+                            issues.push(`${id}: has CONTEXT-DRAFT.md (will pause for discussion)`);
+                    }
+                    if (issues.length > 0) {
+                        ctx.ui.notify(`Pre-flight: ${milestoneIds.length} milestones queued.\n${issues.map((i) => `  ⚠ ${i}`).join("\n")}`, "warning");
+                    }
+                    else {
+                        ctx.ui.notify(`Pre-flight: ${milestoneIds.length} milestones queued. All have full context.`, "info");
+                    }
                 }
             }
         }
+        catch {
+            /* non-fatal */
+        }
+        return true;
+    }
+    catch (err) {
+        releaseSessionLock(base);
+        clearLock(base);
+        throw err;
     }
-    catch { /* non-fatal */ }
-    return true;
 }