gsd-pi 2.78.0 → 2.78.1-dev.42ef05fbe

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

@@ -7,7 +7,6 @@
  */
 import { existsSync, cpSync, readFileSync, readdirSync, mkdirSync, realpathSync, rmSync, unlinkSync, statSync, lstatSync as lstatSyncFn, } from "node:fs";
 import { isAbsolute, join, sep as pathSep } from "node:path";
-import { homedir } from "node:os";
 import { GSDError, GSD_IO_ERROR, GSD_GIT_ERROR } from "./errors.js";
 import { reconcileWorktreeDb, isDbAvailable, getMilestone, getMilestoneSlices, closeDatabase, openDatabase, getDbPath, } from "./gsd-db.js";
 import { atomicWriteSync } from "./atomic-write.js";
@@ -16,14 +15,23 @@ import { safeCopy, safeCopyRecursive } from "./safe-fs.js";
 import { gsdRoot } from "./paths.js";
 import { createWorktree, removeWorktree, resolveGitDir, worktreePath, isInsideWorktreesDir, } from "./worktree-manager.js";
 import { detectWorktreeName, nudgeGitBranchCache, } from "./worktree.js";
+import { isGsdWorktreePath, normalizeWorktreePathForCompare, resolveWorktreeProjectRoot, } from "./worktree-root.js";
 import { MergeConflictError, readIntegrationBranch, RUNTIME_EXCLUSION_PATHS } from "./git-service.js";
 import { debugLog } from "./debug-logger.js";
 import { logWarning, logError } from "./workflow-logger.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
+import { MILESTONE_ID_RE } from "./milestone-ids.js";
 import { nativeGetCurrentBranch, nativeDetectMainBranch, nativeWorkingTreeStatus, nativeAddAllWithExclusions, nativeCommit, nativeCheckoutBranch, nativeMergeSquash, nativeConflictFiles, nativeCheckoutTheirs, nativeAddPaths, nativeRmForce, nativeBranchDelete, nativeBranchForceReset, nativeBranchExists, nativeDiffNumstat, nativeUpdateRef, nativeIsAncestor, nativeMergeAbort, } from "./native-git-bridge.js";
-const gsdHome = process.env.GSD_HOME || join(homedir(), ".gsd");
+import { gsdHome } from "./gsd-home.js";
 const PROJECT_PREFERENCES_FILE = "PREFERENCES.md";
 const LEGACY_PROJECT_PREFERENCES_FILE = "preferences.md";
+const LEGACY_DEEP_SETUP_RUNTIME_UNIT_FILES = new Set([
+    "workflow-preferences-WORKFLOW-PREFS.json",
+    "discuss-project-PROJECT.json",
+    "discuss-requirements-REQUIREMENTS.json",
+    "research-decision-RESEARCH-DECISION.json",
+    "research-project-RESEARCH-PROJECT.json",
+]);
 // ─── Shared Constants & Helpers ─────────────────────────────────────────────
 /**
  * Root-level .gsd/ state files synced between worktree and project root.
@@ -373,7 +381,7 @@ export function syncStateToProjectRoot(worktreePath_, projectRoot, milestoneId)
  * doesn't falsely trigger staleness (#804).
  */
 export function readResourceVersion() {
-    const agentDir = process.env.GSD_CODING_AGENT_DIR || join(gsdHome, "agent");
+    const agentDir = process.env.GSD_CODING_AGENT_DIR || join(gsdHome(), "agent");
     const manifestPath = join(agentDir, "managed-resources.json");
     try {
         const manifest = JSON.parse(readFileSync(manifestPath, "utf-8"));
@@ -431,9 +439,9 @@ export function escapeStaleWorktree(base) {
     // the string-slice heuristic matched the wrong /.gsd/ boundary. This happens
     // when .gsd is a symlink into ~/.gsd/projects/<hash> and process.cwd()
     // resolved through the symlink. Returning ~ would be catastrophic (#1676).
-    const candidateGsd = join(projectRoot, ".gsd").replaceAll("\\", "/");
-    const gsdHomePath = gsdHome.replaceAll("\\", "/");
-    if (candidateGsd === gsdHomePath || candidateGsd.startsWith(gsdHomePath + "/")) {
+    const candidateGsd = normalizeWorktreePathForCompare(join(projectRoot, ".gsd"));
+    const gsdHomeNorm = normalizeWorktreePathForCompare(gsdHome());
+    if (candidateGsd === gsdHomeNorm || candidateGsd.startsWith(gsdHomeNorm + "/")) {
         // Don't chdir to home — return base unchanged.
         // resolveProjectRoot() in worktree.ts has the full git-file-based recovery
         // and will be called by the caller (startAuto → projectRoot()).
@@ -465,6 +473,29 @@ export function cleanStaleRuntimeUnits(gsdRootPath, hasMilestoneSummary) {
         for (const file of readdirSync(runtimeUnitsDir)) {
             if (!file.endsWith(".json"))
                 continue;
+            if (LEGACY_DEEP_SETUP_RUNTIME_UNIT_FILES.has(file)) {
+                try {
+                    unlinkSync(join(runtimeUnitsDir, file));
+                    cleaned++;
+                }
+                catch (err) {
+                    /* non-fatal */
+                    logWarning("worktree", `stale runtime unit unlink failed (${file}): ${err instanceof Error ? err.message : String(err)}`);
+                }
+                continue;
+            }
+            const staleDiscussMatch = file.match(/^discuss-milestone-(.+)\.json$/);
+            if (staleDiscussMatch && !MILESTONE_ID_RE.test(staleDiscussMatch[1])) {
+                try {
+                    unlinkSync(join(runtimeUnitsDir, file));
+                    cleaned++;
+                }
+                catch (err) {
+                    /* non-fatal */
+                    logWarning("worktree", `stale runtime unit unlink failed (${file}): ${err instanceof Error ? err.message : String(err)}`);
+                }
+                continue;
+            }
             const midMatch = file.match(/(M\d+(?:-[a-z0-9]{6})?)/);
             if (!midMatch)
                 continue;
@@ -857,6 +888,11 @@ export function runWorktreePostCreateHook(sourceDir, worktreeDir, hookPath) {
 export function autoWorktreeBranch(milestoneId) {
     return `milestone/${milestoneId}`;
 }
+function normalizeLocalBranchRef(branch) {
+    return branch.startsWith("refs/heads/")
+        ? branch.slice("refs/heads/".length)
+        : branch;
+}
 // ─── Branch-mode Entry ─────────────────────────────────────────────────────
 /**
  * Enter branch isolation mode for a milestone.
@@ -1033,6 +1069,14 @@ function reconcilePlanCheckboxes(projectRoot, wtPath, milestoneId) {
     }
 }
 export function createAutoWorktree(basePath, milestoneId) {
+    basePath = resolveWorktreeProjectRoot(basePath);
+    // Check if repo has commits — git worktree requires a valid HEAD
+    try {
+        execFileSync("git", ["rev-parse", "--verify", "HEAD"], { cwd: basePath, stdio: "pipe" });
+    }
+    catch {
+        throw new GSDError(GSD_GIT_ERROR, `Cannot create worktree: repository has no commits yet. Worktree isolation requires at least one commit.`);
+    }
     const branch = autoWorktreeBranch(milestoneId);
     // Check if the milestone branch already exists — it survives auto-mode
     // stop/pause and contains committed work from prior sessions. If it exists,
@@ -1159,6 +1203,7 @@ function copyPlanningArtifacts(srcBase, wtPath) {
  * the worktree and its branch.
  */
 export function teardownAutoWorktree(originalBasePath, milestoneId, opts = {}) {
+    originalBasePath = resolveWorktreeProjectRoot(originalBasePath);
     const branch = autoWorktreeBranch(milestoneId);
     const { preserveBranch = false } = opts;
     const previousCwd = process.cwd();
@@ -1200,18 +1245,26 @@ export function teardownAutoWorktree(originalBasePath, milestoneId, opts = {}) {
 }
 /**
  * Detect if the process is currently inside an auto-worktree.
- * Checks both module state and git branch prefix.
+ * Uses the current directory structure plus git branch prefix so detection
+ * still works after process restart when module state has been reset.
  */
 export function isInAutoWorktree(basePath) {
-    if (!originalBase)
-        return false;
     const cwd = process.cwd();
-    const resolvedBase = existsSync(basePath) ? realpathSync(basePath) : basePath;
-    const wtDir = join(resolvedBase, ".gsd", "worktrees");
-    if (!cwd.startsWith(wtDir))
+    if (!isGsdWorktreePath(cwd))
         return false;
-    const branch = nativeGetCurrentBranch(cwd);
-    return branch.startsWith("milestone/");
+    const projectRoot = resolveWorktreeProjectRoot(basePath, originalBase);
+    const cwdProjectRoot = resolveWorktreeProjectRoot(cwd, originalBase);
+    if (normalizeWorktreePathForCompare(projectRoot) !==
+        normalizeWorktreePathForCompare(cwdProjectRoot)) {
+        return false;
+    }
+    try {
+        const branch = nativeGetCurrentBranch(cwd);
+        return branch.startsWith("milestone/");
+    }
+    catch {
+        return false;
+    }
 }
 /**
  * Get the filesystem path for an auto-worktree, or null if it doesn't exist
@@ -1222,6 +1275,7 @@ export function isInAutoWorktree(basePath) {
  * mis-detection of leftover directories as active worktrees (#695).
  */
 export function getAutoWorktreePath(basePath, milestoneId) {
+    basePath = resolveWorktreeProjectRoot(basePath);
     const p = worktreePath(basePath, milestoneId);
     if (!existsSync(p))
         return null;
@@ -1248,6 +1302,7 @@ export function getAutoWorktreePath(basePath, milestoneId) {
  * Atomic: chdir + originalBase update in same try block.
  */
 export function enterAutoWorktree(basePath, milestoneId) {
+    basePath = resolveWorktreeProjectRoot(basePath);
     const p = worktreePath(basePath, milestoneId);
     if (!existsSync(p)) {
         throw new GSDError(GSD_IO_ERROR, `Auto-worktree for ${milestoneId} does not exist at ${p}`);
@@ -1286,16 +1341,20 @@ export function enterAutoWorktree(basePath, milestoneId) {
 export function getAutoWorktreeOriginalBase() {
     return originalBase;
 }
+export function _resetAutoWorktreeOriginalBaseForTests() {
+    originalBase = null;
+}
 export function getActiveAutoWorktreeContext() {
     if (!originalBase)
         return null;
     const cwd = process.cwd();
-    const resolvedBase = existsSync(originalBase)
-        ? realpathSync(originalBase)
-        : originalBase;
-    const wtDir = join(resolvedBase, ".gsd", "worktrees");
-    if (!cwd.startsWith(wtDir))
+    if (!isGsdWorktreePath(cwd))
+        return null;
+    const cwdProjectRoot = resolveWorktreeProjectRoot(cwd, originalBase);
+    if (normalizeWorktreePathForCompare(cwdProjectRoot) !==
+        normalizeWorktreePathForCompare(originalBase)) {
         return null;
+    }
     const worktreeName = detectWorktreeName(cwd);
     if (!worktreeName)
         return null;
@@ -1408,6 +1467,10 @@ export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapCont
         }
     }
     // 3. chdir to original base
+    // Note: previousCwd captures the cwd at this point — i.e. the worktree cwd
+    // entering the function. Subsequent throws restore to previousCwd, leaving
+    // the caller in worktree-cwd; callers (worktree-resolver) are responsible
+    // for any further cwd movement on the error path.
     const previousCwd = process.cwd();
     process.chdir(originalBasePath_);
     // 4. Resolve integration branch — prefer milestone metadata, then preferences,
@@ -1422,6 +1485,20 @@ export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapCont
         ? prefs.main_branch
         : undefined;
     const mainBranch = integrationBranch ?? validatedPrefBranch ?? nativeDetectMainBranch(originalBasePath_);
+    // Fail closed when the resolved integration branch is the milestone branch
+    // itself (#5024). Stale or corrupt metadata (e.g. integrationBranch recorded
+    // as "milestone/<MID>") would otherwise let the squash merge resolve to a
+    // self-merge: nothing-to-commit + empty self-diff in the post-merge safety
+    // check (#1792) collapse to a false success, and the worktree-resolver
+    // emits worktree-merged for work that never landed on a distinct
+    // integration branch.
+    if (normalizeLocalBranchRef(mainBranch) === milestoneBranch) {
+        process.chdir(previousCwd);
+        throw new GSDError(GSD_GIT_ERROR, `Resolved integration branch "${mainBranch}" is the same ref as milestone branch ` +
+            `"${milestoneBranch}" — refusing to self-merge. Integration branch metadata is invalid; ` +
+            `set a distinct main_branch in GSD preferences or repair the milestone integration record ` +
+            `before retrying milestone completion.`);
+    }
     // Remove transient project-root state files before any branch or merge
     // operation. Untracked milestone metadata can otherwise block squash merges.
     clearProjectRootStateFiles(originalBasePath_, milestoneId);
@@ -2029,5 +2106,20 @@ export function mergeMilestoneToMain(originalBasePath_, milestoneId, roadmapCont
     // 14. Clear module state
     originalBase = null;
     nudgeGitBranchCache(previousCwd);
+    // 15. Anchor cwd at the project root on success-return. Step 12 removed
+    // the worktree dir; if cwd was inside it, every subsequent process.cwd()
+    // would throw ENOENT and trip auto/run-unit.ts:50's session-failed cancel
+    // path (the de73fb43d regression that closes headless gsd auto). Step 3
+    // already chdir'd here, but defending the success-return contract makes
+    // future maintainers safe against intervening chdir's between step 3 and
+    // here.
+    try {
+        // process.cwd() can throw ENOENT when cwd was removed, so attempt
+        // recovery directly.
+        process.chdir(originalBasePath_);
+    }
+    catch (err) {
+        logWarning("worktree", `chdir to project root after merge failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
     return { commitMessage, pushed, prCreated, codeFilesChanged };
 }

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

@@ -38,7 +38,6 @@ import { deactivateGSD } from "../shared/gsd-phase-state.js";
 import { initMetrics, resetMetrics, getLedger, getProjectTotals, formatCost, formatTokenCount, } from "./metrics.js";
 import { setLogBasePath, logWarning } from "./workflow-logger.js";
 import { preflightCleanRoot, postflightPopStash } from "./clean-root-preflight.js";
-import { homedir } from "node:os";
 import { isAbsolute, join } from "node:path";
 import { pathToFileURL } from "node:url";
 import { readFileSync, existsSync, mkdirSync, writeFileSync, unlinkSync } from "node:fs";
@@ -80,13 +79,13 @@ import { runAutoLoopWithUok } from "./uok/kernel.js";
 import { resolveUokFlags } from "./uok/flags.js";
 import { WorktreeResolver, } from "./worktree-resolver.js";
 import { reorderForCaching } from "./prompt-ordering.js";
-// ─── Session State ─────────────────────────────────────────────────────────
-import { AutoSession, } from "./auto/session.js";
 export { STUB_RECOVERY_THRESHOLD, NEW_SESSION_TIMEOUT_MS, } from "./auto/session.js";
+import { autoSession as s } from "./auto-runtime-state.js";
+import { gsdHome } from "./gsd-home.js";
 // ── ENCAPSULATION INVARIANT ─────────────────────────────────────────────────
 // ALL mutable auto-mode state lives in the AutoSession class (auto/session.ts).
 // This file must NOT declare module-level `let` or `var` variables for state.
-// The single `s` instance below is the only mutable module-level binding.
+// The single shared `s` instance below is the only mutable AutoSession binding.
 //
 // When adding features or fixing bugs:
 //   - New mutable state → add a property to AutoSession, not a module-level variable
@@ -95,7 +94,6 @@ export { STUB_RECOVERY_THRESHOLD, NEW_SESSION_TIMEOUT_MS, } from "./auto/session
 //
 // Tests in auto-session-encapsulation.test.ts enforce this invariant.
 // ─────────────────────────────────────────────────────────────────────────────
-const s = new AutoSession();
 /** Throttle STATE.md rebuilds — at most once per 30 seconds */
 const STATE_REBUILD_MIN_INTERVAL_MS = 30_000;
 function captureProjectRootEnv(projectRoot) {
@@ -180,11 +178,7 @@ export function startAutoDetached(ctx, pi, base, verboseMode, options) {
 }
 /** Returns true if the project is configured for `isolation:worktree` mode. */
 export function shouldUseWorktreeIsolation(basePath) {
-    const prefs = loadEffectiveGSDPreferences(basePath)?.preferences?.git;
-    if (prefs?.isolation === "worktree")
-        return true;
-    // Default is false — worktree isolation requires explicit opt-in
-    return false;
+    return getIsolationMode(basePath) === "worktree";
 }
 /** Crash recovery prompt — set by startAuto, consumed by the main loop */
 /** Pending verification retry — set when gate fails with retries remaining, consumed by autoLoop */
@@ -895,6 +889,19 @@ export async function pauseAuto(ctx, _pi, _errorContext) {
         }
         s.currentUnit = null;
     }
+    // Keep STATE.md aligned with the DB-backed state before releasing pause state.
+    // Without this, an interrupted deep run can leave STATE.md saying "no active
+    // milestone" even after the DB/disk reconciliation has recovered the next unit.
+    if (s.basePath) {
+        try {
+            await rebuildState(s.basePath);
+        }
+        catch (e) {
+            debugLog("pause-rebuild-state-failed", {
+                error: e instanceof Error ? e.message : String(e),
+            });
+        }
+    }
     if (lockBase()) {
         releaseSessionLock(lockBase());
         clearLock(lockBase());
@@ -1297,7 +1304,7 @@ export async function startAuto(ctx, pi, base, verboseMode, options) {
         // tree; deployed extensions live at ~/.gsd/agent/extensions/gsd/ where the
         // relative path resolves to ~/.gsd/agent/resource-loader.js which doesn't exist.
         // Using GSD_PKG_ROOT constructs a correct absolute path in both contexts (#3949).
-        const agentDir = process.env.GSD_CODING_AGENT_DIR || join(process.env.GSD_HOME || homedir(), ".gsd", "agent");
+        const agentDir = process.env.GSD_CODING_AGENT_DIR || join(gsdHome(), "agent");
         const pkgRoot = process.env.GSD_PKG_ROOT;
         const resourceLoaderPath = pkgRoot
             ? pathToFileURL(join(pkgRoot, "dist", "resource-loader.js")).href
@@ -1408,10 +1415,21 @@ const widgetStateAccessors = {
  * Ensure directories, branches, and other prerequisites exist before
  * dispatching a unit. The LLM should never need to mkdir or git checkout.
  */
-function ensurePreconditions(unitType, unitId, base, state) {
+export function ensurePreconditions(unitType, unitId, base, state) {
     const { milestone: mid, slice: sid } = parseUnitId(unitId);
     const mDir = resolveMilestonePath(base, mid);
     if (!mDir) {
+        // Fix #4996: When dispatching a slice unit against an unrecognised milestone,
+        // only create the directory if the milestone has a DB row.
+        // Without this guard, forward-referenced unit IDs (e.g. from REQUIREMENTS.md)
+        // silently scaffold empty stub directories that later skew nextMilestoneId.
+        if (sid !== undefined) {
+            const hasDbRow = isDbAvailable() && getMilestone(mid) != null;
+            if (!hasDbRow) {
+                logWarning("engine", `ensurePreconditions: skipping mkdir for unrecognised milestone ${mid} referenced by slice unit ${unitId} — no DB row exists`, { file: "auto.ts" });
+                return;
+            }
+        }
         const newDir = join(milestonesDir(base), mid);
         mkdirSync(join(newDir, "slices"), { recursive: true });
     }
@@ -1432,15 +1450,18 @@ function ensurePreconditions(unitType, unitId, base, state) {
     }
 }
 export async function dispatchHookUnit(ctx, pi, hookName, triggerUnitType, triggerUnitId, hookPrompt, hookModel, targetBasePath) {
+    const wasActive = s.active;
+    const previousBasePath = s.basePath;
+    const previousCurrentUnit = s.currentUnit ? { ...s.currentUnit } : null;
     if (!s.active) {
         s.active = true;
         s.stepMode = true;
         s.cmdCtx = ctx;
-        s.basePath = targetBasePath;
         s.autoStartTime = Date.now();
         s.currentUnit = null;
         s.pendingQuickTasks = [];
     }
+    s.basePath = targetBasePath;
     const hookUnitType = `hook/${hookName}`;
     const hookStartedAt = Date.now();
     s.currentUnit = {
@@ -1448,6 +1469,27 @@ export async function dispatchHookUnit(ctx, pi, hookName, triggerUnitType, trigg
         id: triggerUnitId,
         startedAt: hookStartedAt,
     };
+    // Ensure cwd matches basePath BEFORE newSession() captures it (#1389).
+    // newSession() snapshots process.cwd() during construction; chdir-ing
+    // afterward leaves the session rooted to whatever cwd was when the call
+    // was made. Must be synchronous — no awaits between chdir and newSession.
+    try {
+        if (process.cwd() !== s.basePath)
+            process.chdir(s.basePath);
+    }
+    catch (err) {
+        const msg = `Failed to chdir before hook newSession (basePath: ${s.basePath}): ${err instanceof Error ? err.message : String(err)}`;
+        logWarning("engine", msg, { file: "auto.ts", basePath: s.basePath, error: err instanceof Error ? err.message : String(err) });
+        ctx.ui.notify(`${msg}. Cancelling hook dispatch to avoid running in the wrong directory.`, "error");
+        if (wasActive) {
+            s.basePath = previousBasePath;
+            s.currentUnit = previousCurrentUnit;
+        }
+        else {
+            s.reset();
+        }
+        return false;
+    }
     const result = await s.cmdCtx.newSession();
     if (result.cancelled) {
         await stopAuto(ctx, pi);
@@ -1490,14 +1532,6 @@ export async function dispatchHookUnit(ctx, pi, hookName, triggerUnitType, trigg
     }, hookHardTimeoutMs);
     ctx.ui.setStatus("gsd-auto", s.stepMode ? "next" : "auto");
     ctx.ui.notify(`Running post-unit hook: ${hookName}`, "info");
-    // Ensure cwd matches basePath before hook dispatch (#1389)
-    try {
-        if (process.cwd() !== s.basePath)
-            process.chdir(s.basePath);
-    }
-    catch (err) {
-        logWarning("engine", `chdir failed before hook dispatch: ${err instanceof Error ? err.message : String(err)}`, { file: "auto.ts" });
-    }
     debugLog("dispatchHookUnit", {
         phase: "send-message",
         promptLength: hookPrompt.length,

package/dist/resources/extensions/gsd/bootstrap/agent-end-recovery.js

@@ -1,11 +1,12 @@
 import { logWarning } from "../workflow-logger.js";
-import { checkAutoStartAfterDiscuss, maybeHandleReadyPhraseWithoutFiles, maybeHandleEmptyIntentTurn, resetEmptyTurnCounter, } from "../guided-flow.js";
+import { checkDeepProjectSetupAfterTurn, checkAutoStartAfterDiscuss, maybeHandleReadyPhraseWithoutFiles, maybeHandleEmptyIntentTurn, resetEmptyTurnCounter, } from "../guided-flow.js";
 import { clearPathCache } from "../paths.js";
 import { getAutoDashboardData, getAutoModeStartModel, isAutoActive, pauseAuto, setCurrentDispatchedModelId } from "../auto.js";
 import { getNextFallbackModel, resolveModelWithFallbacksForUnit } from "../preferences.js";
 import { pauseAutoForProviderError } from "../provider-error-pause.js";
 import { isSessionSwitchInFlight, resolveAgentEnd } from "../auto-loop.js";
 import { resolveModelId } from "../auto-model-selection.js";
+import { resolveProjectRoot } from "../worktree.js";
 import { clearDiscussionFlowState } from "./write-gate.js";
 import { resumeAutoAfterProviderDelay } from "./provider-error-resume.js";
 import { classifyError, createRetryState, resetRetryState, isTransient, } from "../error-classifier.js";
@@ -30,6 +31,14 @@ export const MAX_TRANSIENT_AUTO_RESUMES = 8;
 export function resetTransientRetryState() {
     resetRetryState(retryState);
 }
+function resolveAgentEndBasePath() {
+    try {
+        return resolveProjectRoot(process.cwd());
+    }
+    catch {
+        return undefined;
+    }
+}
 async function pauseTransientWithBackoff(cls, pi, ctx, errorDetail, isRateLimit) {
     retryState.consecutiveTransientCount += 1;
     const baseRetryAfterMs = "retryAfterMs" in cls ? cls.retryAfterMs : 15_000;
@@ -67,6 +76,15 @@ export async function handleAgentEnd(pi, event, ctx) {
     // falsely report files as missing — producing a spurious "ready signal
     // rejected" loop even though the files are on disk.
     clearPathCache();
+    try {
+        if (await checkDeepProjectSetupAfterTurn(event, ctx, resolveAgentEndBasePath())) {
+            return;
+        }
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        logWarning("bootstrap", `checkDeepProjectSetupAfterTurn failed: ${message}`);
+    }
     if (checkAutoStartAfterDiscuss()) {
         clearDiscussionFlowState();
         return;