gsd-pi 2.35.0-dev.55dcc60 → 2.35.0-dev.6179610

package/src/resources/extensions/get-secrets-from-user.ts

@@ -11,9 +11,9 @@ import { existsSync, statSync } from "node:fs";
 import { resolve } from "node:path";
 
 import type { ExtensionAPI, Theme } from "@gsd/pi-coding-agent";
-import { CURSOR_MARKER, Editor, type EditorTheme, Key, matchesKey, Text, truncateToWidth, wrapTextWithAnsi } from "@gsd/pi-tui";
+import { Editor, type EditorTheme, Key, matchesKey, Text, truncateToWidth, wrapTextWithAnsi } from "@gsd/pi-tui";
 import { Type } from "@sinclair/typebox";
-import { makeUI, type ProgressStatus } from "./shared/mod.js";
+import { makeUI, maskEditorLine, type ProgressStatus } from "./shared/mod.js";
 import { parseSecretsManifest, formatSecretsManifest } from "./gsd/files.js";
 import { resolveMilestoneFile } from "./gsd/paths.js";
 import type { SecretsManifestEntry } from "./gsd/types.js";
@@ -42,39 +42,6 @@ function maskPreview(value: string): string {
 	return `${value.slice(0, 4)}${"*".repeat(Math.max(4, value.length - 8))}${value.slice(-4)}`;
 }
 
-/**
- * Replace editor visible text with masked characters while preserving ANSI cursor/sequencer codes.
- */
-function maskEditorLine(line: string): string {
-	// Keep border / metadata lines readable.
-	if (line.startsWith("─")) {
-		return line;
-	}
-
-	let output = "";
-	let i = 0;
-	while (i < line.length) {
-		if (line.startsWith(CURSOR_MARKER, i)) {
-			output += CURSOR_MARKER;
-			i += CURSOR_MARKER.length;
-			continue;
-		}
-
-		const ansiMatch = /^\x1b\[[0-9;]*m/.exec(line.slice(i));
-		if (ansiMatch) {
-			output += ansiMatch[0];
-			i += ansiMatch[0].length;
-			continue;
-		}
-
-		const ch = line[i] as string;
-		output += ch === " " ? " " : "*";
-		i += 1;
-	}
-
-	return output;
-}
-
 function shellEscapeSingle(value: string): string {
 	return `'${value.replace(/'/g, `'\\''`)}'`;
 }

package/src/resources/extensions/google-search/index.ts

@@ -411,6 +411,13 @@ export default function (pi: ExtensionAPI) {
 		},
 	});
 
+	// ── Session cleanup ─────────────────────────────────────────────────────
+
+	pi.on("session_shutdown", async () => {
+		resultCache.clear();
+		client = null;
+	});
+
 	// ── Startup notification ─────────────────────────────────────────────────
 
 	pi.on("session_start", async (_event, ctx) => {

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

@@ -12,14 +12,16 @@
 import type { GSDState } from "./types.js";
 import type { GSDPreferences } from "./preferences.js";
 import type { UatType } from "./files.js";
-import { loadFile, extractUatType, loadActiveOverrides } from "./files.js";
+import { loadFile, extractUatType, loadActiveOverrides, parseRoadmap } from "./files.js";
 import {
   resolveMilestoneFile,
   resolveMilestonePath,
   resolveSliceFile,
+  resolveSlicePath,
   resolveTaskFile,
   relSliceFile,
   buildMilestoneFileName,
+  buildSliceFileName,
 } from "./paths.js";
 import { existsSync, mkdirSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
@@ -369,6 +371,30 @@ const DISPATCH_RULES: DispatchRule[] = [
     name: "validating-milestone → validate-milestone",
     match: async ({ state, mid, midTitle, basePath, prefs }) => {
       if (state.phase !== "validating-milestone") return null;
+
+      // Safety guard (#1368): verify all roadmap slices have SUMMARY files before
+      // allowing milestone validation. If any slice lacks a summary, the milestone
+      // is not genuinely complete — something skipped earlier slices.
+      const roadmapFile = resolveMilestoneFile(basePath, mid, "ROADMAP");
+      const roadmapContent = roadmapFile ? await loadFile(roadmapFile) : null;
+      if (roadmapContent) {
+        const roadmap = parseRoadmap(roadmapContent);
+        const missingSlices: string[] = [];
+        for (const slice of roadmap.slices) {
+          const summaryPath = resolveSliceFile(basePath, mid, slice.id, "SUMMARY");
+          if (!summaryPath || !existsSync(summaryPath)) {
+            missingSlices.push(slice.id);
+          }
+        }
+        if (missingSlices.length > 0) {
+          return {
+            action: "stop",
+            reason: `Cannot validate milestone ${mid}: slices ${missingSlices.join(", ")} are missing SUMMARY files. These slices may have been skipped.`,
+            level: "error",
+          };
+        }
+      }
+
       // Skip preference: write a minimal pass-through VALIDATION file
       if (prefs?.phases?.skip_milestone_validation) {
         const mDir = resolveMilestonePath(basePath, mid);
@@ -404,6 +430,28 @@ const DISPATCH_RULES: DispatchRule[] = [
     name: "completing-milestone → complete-milestone",
     match: async ({ state, mid, midTitle, basePath }) => {
       if (state.phase !== "completing-milestone") return null;
+
+      // Safety guard (#1368): verify all roadmap slices have SUMMARY files.
+      const roadmapFile = resolveMilestoneFile(basePath, mid, "ROADMAP");
+      const roadmapContent = roadmapFile ? await loadFile(roadmapFile) : null;
+      if (roadmapContent) {
+        const roadmap = parseRoadmap(roadmapContent);
+        const missingSlices: string[] = [];
+        for (const slice of roadmap.slices) {
+          const summaryPath = resolveSliceFile(basePath, mid, slice.id, "SUMMARY");
+          if (!summaryPath || !existsSync(summaryPath)) {
+            missingSlices.push(slice.id);
+          }
+        }
+        if (missingSlices.length > 0) {
+          return {
+            action: "stop",
+            reason: `Cannot complete milestone ${mid}: slices ${missingSlices.join(", ")} are missing SUMMARY files. Run /gsd doctor to diagnose.`,
+            level: "error",
+          };
+        }
+      }
+
       return {
         action: "dispatch",
         unitType: "complete-milestone",

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

@@ -221,6 +221,15 @@ export async function runUnit(
     s.pendingResolve = resolve;
   });
 
+  // Ensure cwd matches basePath before dispatch (#1389).
+  // async_bash and background jobs can drift cwd away from the worktree.
+  // Realigning here prevents commits from landing on the wrong branch.
+  try {
+    if (process.cwd() !== s.basePath) {
+      process.chdir(s.basePath);
+    }
+  } catch { /* non-fatal — chdir may fail if dir was removed */ }
+
   // ── Send the prompt ──
   debugLog("runUnit", { phase: "send-message", unitType, unitId });
 
@@ -344,6 +353,7 @@ export interface LoopDeps {
   getManifestStatus: (
     basePath: string,
     mid: string | undefined,
+    projectRoot?: string,
   ) => Promise<{ pending: unknown[] } | null>;
   collectSecretsFromManifest: (
     basePath: string,
@@ -983,7 +993,7 @@ export async function autoLoop(
 
       // Secrets re-check gate
       try {
-        const manifestStatus = await deps.getManifestStatus(s.basePath, mid);
+        const manifestStatus = await deps.getManifestStatus(s.basePath, mid, s.originalBasePath);
         if (manifestStatus && manifestStatus.pending.length > 0) {
           const result = await deps.collectSecretsFromManifest(
             s.basePath,

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

@@ -8,6 +8,8 @@
  */
 
 import type { ExtensionContext } from "@gsd/pi-coding-agent";
+import { parseUnitId } from "./unit-id.js";
+import { atomicWriteSync } from "./atomic-write.js";
 import { clearUnitRuntimeRecord } from "./unit-runtime.js";
 import { clearParseCache, parseRoadmap, parsePlan } from "./files.js";
 import { isValidationTerminal } from "./state.js";
@@ -35,6 +37,7 @@ import {
   clearPathCache,
   resolveGsdRootFile,
 } from "./paths.js";
+import { markSliceDoneInRoadmap } from "./roadmap-mutations.js";
 import {
   existsSync,
   mkdirSync,
@@ -499,6 +502,42 @@ export async function selfHealRuntimeRecords(
     for (const record of records) {
       const { unitType, unitId } = record;
 
+      // Case 0: complete-slice with SUMMARY + UAT but unchecked roadmap (#1350).
+      // If a complete-slice was interrupted after writing artifacts but before
+      // flipping the roadmap checkbox, the verification fails and the dispatch
+      // loop relaunches the same unit forever. Auto-fix the checkbox.
+      if (unitType === "complete-slice") {
+        const { milestone: mid, slice: sid } = parseUnitId(unitId);
+        if (mid && sid) {
+          const dir = resolveSlicePath(base, mid, sid);
+          if (dir) {
+            const summaryPath = join(dir, buildSliceFileName(sid, "SUMMARY"));
+            const uatPath = join(dir, buildSliceFileName(sid, "UAT"));
+            if (existsSync(summaryPath) && existsSync(uatPath)) {
+              const roadmapFile = resolveMilestoneFile(base, mid, "ROADMAP");
+              if (roadmapFile && existsSync(roadmapFile)) {
+                try {
+                  const roadmapContent = readFileSync(roadmapFile, "utf-8");
+                  const roadmap = parseRoadmap(roadmapContent);
+                  const slice = (roadmap.slices ?? []).find(s => s.id === sid);
+                  if (slice && !slice.done) {
+                    // Auto-fix: flip the checkbox using shared utility
+                    if (markSliceDoneInRoadmap(base, mid, sid)) {
+                      ctx.ui.notify(
+                        `Self-heal: marked ${sid} done in roadmap (SUMMARY + UAT exist but checkbox was stale).`,
+                        "info",
+                      );
+                    }
+                  }
+                } catch {
+                  // Roadmap parse failure — don't block self-heal
+                }
+              }
+            }
+          }
+        }
+      }
+
       // Clear stale dispatched records (dispatched > 1h ago, process crashed)
       const age = now - (record.startedAt ?? 0);
       if (record.phase === "dispatched" && age > STALE_THRESHOLD_MS) {

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

@@ -20,6 +20,8 @@ import {
   resolveSkillDiscoveryMode,
   getIsolationMode,
 } from "./preferences.js";
+import { ensureGsdSymlink } from "./repo-identity.js";
+import { migrateToExternalState, recoverFailedMigration } from "./migrate-external.js";
 import { collectSecretsFromManifest } from "../get-secrets-from-user.js";
 import { gsdRoot, resolveMilestoneFile, milestonesDir } from "./paths.js";
 import { invalidateAllCaches } from "./cache.js";
@@ -92,6 +94,13 @@ export interface BootstrapDeps {
  * Returns false if the bootstrap aborted (e.g., guided flow returned,
  * concurrent session detected). Returns true when ready to dispatch.
  */
+
+/** Guard: tracks consecutive bootstrap attempts that found phase === "complete".
+ *  Prevents the recursive dialog loop described in #1348 where
+ *  bootstrapAutoSession → showSmartEntry → checkAutoStartAfterDiscuss → startAuto
+ *  cycles indefinitely when the discuss workflow doesn't produce a milestone. */
+let _consecutiveCompleteBootstraps = 0;
+const MAX_CONSECUTIVE_COMPLETE_BOOTSTRAPS = 2;
 export async function bootstrapAutoSession(
   s: AutoSession,
   ctx: ExtensionCommandContext,
@@ -128,7 +137,20 @@ export async function bootstrapAutoSession(
       nativeInit(base, mainBranch);
     }
 
-    // Ensure .gitignore has baseline patterns
+    // Migrate legacy in-project .gsd/ to external state directory.
+    // Migration MUST run before ensureGitignore to avoid adding ".gsd" to
+    // .gitignore when .gsd/ is git-tracked (data-loss bug #1364).
+    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);
+
+    // Ensure .gitignore has baseline patterns.
+    // ensureGitignore checks for git-tracked .gsd/ files and skips the
+    // ".gsd" pattern if the project intentionally tracks .gsd/ in git.
     const gitPrefs = loadEffectiveGSDPreferences()?.preferences?.git;
     const commitDocs = gitPrefs?.commit_docs;
     const manageGitignore = gitPrefs?.manage_gitignore;
@@ -286,6 +308,20 @@ export async function bootstrapAutoSession(
     if (!hasSurvivorBranch) {
       // No active work — start a new milestone via discuss flow
       if (!state.activeMilestone || state.phase === "complete") {
+        // Guard against recursive dialog loop (#1348):
+        // If we've entered this branch multiple times in quick succession,
+        // the discuss workflow isn't producing a milestone. Break the cycle.
+        _consecutiveCompleteBootstraps++;
+        if (_consecutiveCompleteBootstraps > MAX_CONSECUTIVE_COMPLETE_BOOTSTRAPS) {
+          _consecutiveCompleteBootstraps = 0;
+          ctx.ui.notify(
+            "All milestones are complete and the discussion didn't produce a new one. " +
+            "Run /gsd to start a new milestone manually.",
+            "warning",
+          );
+          return releaseLockAndReturn();
+        }
+
         const { showSmartEntry } = await import("./guided-flow.js");
         await showSmartEntry(ctx, pi, base, { step: requestedStepMode });
 
@@ -296,6 +332,7 @@ export async function bootstrapAutoSession(
           postState.phase !== "complete" &&
           postState.phase !== "pre-planning"
         ) {
+          _consecutiveCompleteBootstraps = 0; // Successfully advanced past "complete"
           state = postState;
         } else if (
           postState.activeMilestone &&
@@ -352,6 +389,9 @@ export async function bootstrapAutoSession(
       return releaseLockAndReturn();
     }
 
+    // Successfully resolved an active milestone — reset the re-entry guard
+    _consecutiveCompleteBootstraps = 0;
+
     // ── Initialize session state ──
     s.active = true;
     s.stepMode = requestedStepMode;
@@ -484,7 +524,7 @@ export async function bootstrapAutoSession(
     // Secrets collection gate
     const mid = state.activeMilestone!.id;
     try {
-      const manifestStatus = await getManifestStatus(base, mid);
+      const manifestStatus = await getManifestStatus(base, mid, s.originalBasePath || base);
       if (manifestStatus && manifestStatus.pending.length > 0) {
         const result = await collectSecretsFromManifest(base, mid, ctx);
         if (

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

@@ -127,7 +127,7 @@ import {
   formatTokenCount,
 } from "./metrics.js";
 import { join } from "node:path";
-import { readFileSync, existsSync, mkdirSync } from "node:fs";
+import { readFileSync, existsSync, mkdirSync, writeFileSync, unlinkSync } from "node:fs";
 import { atomicWriteSync } from "./atomic-write.js";
 import {
   autoCommitCurrentBranch,
@@ -554,6 +554,13 @@ export async function stopAuto(
   resetRoutingHistory();
   resetHookState();
   if (s.basePath) clearPersistedHookState(s.basePath);
+
+  // Remove paused-session metadata if present (#1383)
+  try {
+    const pausedPath = join(gsdRoot(s.originalBasePath || s.basePath), "runtime", "paused-session.json");
+    if (existsSync(pausedPath)) unlinkSync(pausedPath);
+  } catch { /* non-fatal */ }
+
   s.active = false;
   s.paused = false;
   s.stepMode = false;
@@ -607,8 +614,32 @@ export async function pauseAuto(
 
   s.pausedSessionFile = ctx?.sessionManager?.getSessionFile() ?? null;
 
-  if (lockBase()) clearLock(lockBase());
-  if (lockBase()) releaseSessionLock(lockBase());
+  // Persist paused-session metadata so resume survives /exit (#1383).
+  // The fresh-start bootstrap checks for this file and restores worktree context.
+  try {
+    const pausedMeta = {
+      milestoneId: s.currentMilestoneId,
+      worktreePath: isInAutoWorktree(s.basePath) ? s.basePath : null,
+      originalBasePath: s.originalBasePath,
+      stepMode: s.stepMode,
+      pausedAt: new Date().toISOString(),
+      sessionFile: s.pausedSessionFile,
+    };
+    const runtimeDir = join(gsdRoot(s.originalBasePath || s.basePath), "runtime");
+    mkdirSync(runtimeDir, { recursive: true });
+    writeFileSync(
+      join(runtimeDir, "paused-session.json"),
+      JSON.stringify(pausedMeta, null, 2),
+      "utf-8",
+    );
+  } catch {
+    // Non-fatal — resume will still work via full bootstrap, just without worktree context
+  }
+
+  if (lockBase()) {
+    releaseSessionLock(lockBase());
+    clearLock(lockBase());
+  }
 
   deregisterSigtermHandler();
 
@@ -792,6 +823,30 @@ export async function startAuto(
   base = escapeStaleWorktree(base);
 
   // 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 pausedPath = join(gsdRoot(base), "runtime", "paused-session.json");
+      if (existsSync(pausedPath)) {
+        const meta = JSON.parse(readFileSync(pausedPath, "utf-8"));
+        if (meta.milestoneId) {
+          s.currentMilestoneId = meta.milestoneId;
+          s.originalBasePath = meta.originalBasePath || base;
+          s.stepMode = meta.stepMode ?? requestedStepMode;
+          s.paused = true;
+          // Clean up the persisted file — we're consuming it
+          try { unlinkSync(pausedPath); } catch { /* non-fatal */ }
+          ctx.ui.notify(
+            `Resuming paused session for ${meta.milestoneId}${meta.worktreePath ? ` (worktree)` : ""}.`,
+            "info",
+          );
+        }
+      }
+    } catch {
+      // Malformed or missing — proceed with fresh bootstrap
+    }
+  }
+
   if (s.paused) {
     const resumeLock = acquireSessionLock(base);
     if (!resumeLock.acquired) {
@@ -1145,6 +1200,9 @@ export async function dispatchHookUnit(
   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 {}
+
   debugLog("dispatchHookUnit", {
     phase: "send-message",
     promptLength: hookPrompt.length,

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

@@ -24,7 +24,7 @@ import { projectRoot } from "./commands.js";
 import { loadPrompt } from "./prompt-loader.js";
 
 export function dispatchDoctorHeal(pi: ExtensionAPI, scope: string | undefined, reportText: string, structuredIssues: string): void {
-  const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(process.env.HOME ?? "~", ".pi", "GSD-WORKFLOW.md");
+  const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(process.env.HOME ?? "~", ".gsd", "agent", "GSD-WORKFLOW.md");
   const workflow = readFileSync(workflowPath, "utf-8");
   const prompt = loadPrompt("doctor-heal", {
     doctorSummary: reportText,
@@ -187,7 +187,7 @@ export async function handleTriage(ctx: ExtensionCommandContext, pi: ExtensionAP
     roadmapContext: roadmapContext || "(no active roadmap)",
   });
 
-  const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(process.env.HOME ?? "~", ".pi", "GSD-WORKFLOW.md");
+  const workflowPath = process.env.GSD_WORKFLOW_PATH ?? join(process.env.HOME ?? "~", ".gsd", "agent", "GSD-WORKFLOW.md");
   const workflow = readFileSync(workflowPath, "utf-8");
 
   pi.sendMessage(

package/src/resources/extensions/gsd/commands-rate.ts

@@ -0,0 +1,55 @@
+/**
+ * /gsd rate — Submit feedback on the last unit's model tier assignment.
+ * Feeds into the adaptive routing history so future dispatches improve.
+ */
+
+import type { ExtensionCommandContext } from "@gsd/pi-coding-agent";
+import { loadLedgerFromDisk } from "./metrics.js";
+import { recordFeedback, initRoutingHistory } from "./routing-history.js";
+import type { ComplexityTier } from "./complexity-classifier.js";
+
+const VALID_RATINGS = new Set(["over", "under", "ok"]);
+
+export async function handleRate(
+  args: string,
+  ctx: ExtensionCommandContext,
+  basePath: string,
+): Promise<void> {
+  const rating = args.trim().toLowerCase();
+
+  if (!rating || !VALID_RATINGS.has(rating)) {
+    ctx.ui.notify(
+      "Usage: /gsd rate <over|ok|under>\n" +
+      "  over  — model was overpowered for that task (encourage cheaper)\n" +
+      "  ok    — model was appropriate\n" +
+      "  under — model was too weak (encourage stronger)",
+      "info",
+    );
+    return;
+  }
+
+  const ledger = loadLedgerFromDisk(basePath);
+  if (!ledger || ledger.units.length === 0) {
+    ctx.ui.notify("No completed units found — nothing to rate.", "warning");
+    return;
+  }
+
+  const lastUnit = ledger.units[ledger.units.length - 1];
+  const tier = lastUnit.tier as ComplexityTier | undefined;
+
+  if (!tier) {
+    ctx.ui.notify(
+      "Last unit has no tier data (dynamic routing was not active). Rating skipped.",
+      "warning",
+    );
+    return;
+  }
+
+  initRoutingHistory(basePath);
+  recordFeedback(lastUnit.type, lastUnit.id, tier, rating as "over" | "under" | "ok");
+
+  ctx.ui.notify(
+    `Recorded "${rating}" for ${lastUnit.type}/${lastUnit.id} at tier ${tier}.`,
+    "info",
+  );
+}

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

@@ -89,6 +89,7 @@ export function registerGSDCommand(pi: ExtensionAPI): void {
         { cmd: "triage", desc: "Manually trigger triage of pending captures" },
         { cmd: "dispatch", desc: "Dispatch a specific phase directly" },
         { cmd: "history", desc: "View execution history" },
+        { cmd: "rate", desc: "Rate last unit's model tier (over/ok/under) — improves adaptive routing" },
         { cmd: "undo", desc: "Revert last completed unit" },
         { cmd: "skip", desc: "Prevent a unit from auto-mode dispatch" },
         { cmd: "export", desc: "Export milestone/slice results" },
@@ -566,6 +567,12 @@ export async function handleGSDCommand(
         return;
       }
 
+      if (trimmed === "rate" || trimmed.startsWith("rate ")) {
+        const { handleRate } = await import("./commands-rate.js");
+        await handleRate(trimmed.replace(/^rate\s*/, "").trim(), ctx, projectRoot());
+        return;
+      }
+
       if (trimmed.startsWith("skip ")) {
         await handleSkip(trimmed.replace(/^skip\s*/, "").trim(), ctx, projectRoot());
         return;

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

@@ -180,26 +180,36 @@ function checkPortConflicts(basePath: string): EnvironmentCheckResult[] {
   const portsToCheck = new Set<number>();
   const pkgPath = join(basePath, "package.json");
 
-  if (existsSync(pkgPath)) {
-    try {
-      const pkg = JSON.parse(readFileSync(pkgPath, "utf-8"));
-      const scripts = pkg.scripts ?? {};
-      const scriptText = Object.values(scripts).join(" ");
-
-      // Look for --port NNNN, -p NNNN, PORT=NNNN, :NNNN patterns
-      const portMatches = scriptText.matchAll(/(?:--port\s+|(?:^|[^a-z])PORT[=:]\s*|-p\s+|:)(\d{4,5})\b/gi);
-      for (const m of portMatches) {
-        const port = parseInt(m[1], 10);
-        if (port >= 1024 && port <= 65535) portsToCheck.add(port);
-      }
-    } catch {
-      // parse failed — use defaults
+  if (!existsSync(pkgPath)) {
+    // No package.json — this isn't a Node.js project. Skip port checks
+    // entirely to avoid false positives from system services (e.g., macOS
+    // AirPlay Receiver on port 5000). (#1381)
+    return [];
+  }
+
+  try {
+    const pkg = JSON.parse(readFileSync(pkgPath, "utf-8"));
+    const scripts = pkg.scripts ?? {};
+    const scriptText = Object.values(scripts).join(" ");
+
+    // Look for --port NNNN, -p NNNN, PORT=NNNN, :NNNN patterns
+    const portMatches = scriptText.matchAll(/(?:--port\s+|(?:^|[^a-z])PORT[=:]\s*|-p\s+|:)(\d{4,5})\b/gi);
+    for (const m of portMatches) {
+      const port = parseInt(m[1], 10);
+      if (port >= 1024 && port <= 65535) portsToCheck.add(port);
     }
+  } catch {
+    // parse failed — skip port checks rather than using defaults
+    return [];
   }
 
-  // If no ports found in scripts, check common defaults
+  // If no ports found in scripts, check common defaults.
+  // Filter out port 5000 on macOS — AirPlay Receiver uses it by default (#1381).
   if (portsToCheck.size === 0) {
-    for (const p of DEFAULT_DEV_PORTS) portsToCheck.add(p);
+    for (const p of DEFAULT_DEV_PORTS) {
+      if (p === 5000 && process.platform === "darwin") continue;
+      portsToCheck.add(p);
+    }
   }
 
   for (const port of portsToCheck) {

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

@@ -590,7 +590,8 @@ export async function loadFile(path: string): Promise<string | null> {
   try {
     return await fs.readFile(path, 'utf-8');
   } catch (err: unknown) {
-    if ((err as NodeJS.ErrnoException).code === 'ENOENT') return null;
+    const code = (err as NodeJS.ErrnoException).code;
+    if (code === 'ENOENT' || code === 'EISDIR') return null;
     throw err;
   }
 }
@@ -804,7 +805,7 @@ export async function inlinePriorMilestoneSummary(mid: string, base: string): Pr
  * file not on disk) - callers can distinguish "no manifest" from "empty manifest".
  */
 export async function getManifestStatus(
-  base: string, milestoneId: string,
+  base: string, milestoneId: string, projectRoot?: string,
 ): Promise<ManifestStatus | null> {
   const resolvedPath = resolveMilestoneFile(base, milestoneId, 'SECRETS');
   if (!resolvedPath) return null;
@@ -814,9 +815,18 @@ export async function getManifestStatus(
 
   const manifest = parseSecretsManifest(content);
   const keys = manifest.entries.map(e => e.key);
+
+  // Check both the base path .env AND the project root .env (#1387).
+  // In worktree mode, base is the worktree path which may not have .env.
+  // The project root's .env is where the user actually defined their keys.
   const existingKeys = await checkExistingEnvKeys(keys, resolve(base, '.env'));
   const existingSet = new Set(existingKeys);
 
+  if (projectRoot && projectRoot !== base) {
+    const rootKeys = await checkExistingEnvKeys(keys, resolve(projectRoot, '.env'));
+    for (const k of rootKeys) existingSet.add(k);
+  }
+
   const result: ManifestStatus = {
     pending: [],
     collected: [],