gsd-pi 2.79.0-dev.ece5fd8ba → 2.80.0-dev.0aaa4fc17

package/src/resources/extensions/gsd/auto-runtime-state.ts

@@ -16,14 +16,21 @@ export type AutoRuntimeSnapshot = {
   paused: boolean;
   currentUnit: CurrentUnit | null;
   basePath: string;
+  orchestrationPhase?: "idle" | "running" | "paused" | "stopped" | "error";
+  orchestrationTransitionCount?: number;
+  orchestrationLastTransitionAt?: number;
 };
 
 export function getAutoRuntimeSnapshot(): AutoRuntimeSnapshot {
+  const orchestrationStatus = autoSession.orchestration?.getStatus();
   return {
     active: autoSession.active,
     paused: autoSession.paused,
     currentUnit: autoSession.currentUnit ? { ...autoSession.currentUnit } : null,
     basePath: autoSession.basePath,
+    orchestrationPhase: orchestrationStatus?.phase,
+    orchestrationTransitionCount: orchestrationStatus?.transitionCount,
+    orchestrationLastTransitionAt: orchestrationStatus?.lastTransitionAt,
   };
 }
 

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

@@ -664,12 +664,13 @@ export async function bootstrapAutoSession(
     }
 
     const effectivePrefs = loadEffectiveGSDPreferences(base)?.preferences;
-    const deepProjectStagePending = !hasSurvivorBranch
-      ? (await import("./auto-dispatch.js")).hasPendingDeepStage(
-          effectivePrefs,
-          base,
-        )
-      : false;
+    const { shouldRunDeepProjectSetup } = await import("./auto-dispatch.js");
+    const deepProjectStagePending = shouldRunDeepProjectSetup(
+      state,
+      effectivePrefs,
+      base,
+      { hasSurvivorBranch },
+    );
 
     if (deepProjectStagePending) {
       // Deep project-level setup runs before the first milestone exists. Let

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

@@ -1,3 +1,6 @@
+// Project/App: GSD-2
+// File Purpose: Post-unit verification gate for GSD auto-mode units.
+
 /**
  * Post-unit verification gate for auto-mode.
  *
@@ -14,7 +17,8 @@ import type { ExtensionContext, ExtensionAPI } from "@gsd/pi-coding-agent";
 import { mkdirSync, writeFileSync } from "node:fs";
 import { resolveSliceFile, resolveSlicePath, resolveMilestoneFile } from "./paths.js";
 import { parseUnitId } from "./unit-id.js";
-import { isDbAvailable, getTask, getSliceTasks, getMilestoneSlices, type TaskRow } from "./gsd-db.js";
+import { isDbAvailable, getTask, getSliceTasks, getMilestoneSlices } from "./gsd-db.js";
+import type { TaskRow } from "./db-task-slice-rows.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
 import { extractVerdict } from "./verdict-parser.js";
 import { isClosedStatus } from "./status-guards.js";

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

@@ -1,3 +1,6 @@
+// Project/App: GSD-2
+// File Purpose: Auto-mode worktree lifecycle, merge, and cleanup management.
+
 /**
  * GSD Auto-Worktree -- lifecycle management for auto-mode worktrees.
  *
@@ -18,7 +21,7 @@ import {
   statSync,
   lstatSync as lstatSyncFn,
 } from "node:fs";
-import { isAbsolute, join, sep as pathSep } from "node:path";
+import { isAbsolute, join, relative, sep as pathSep } from "node:path";
 import { GSDError, GSD_IO_ERROR, GSD_GIT_ERROR } from "./errors.js";
 import {
   reconcileWorktreeDb,
@@ -50,7 +53,8 @@ import {
   normalizeWorktreePathForCompare,
   resolveWorktreeProjectRoot,
 } from "./worktree-root.js";
-import { MergeConflictError, readIntegrationBranch, RUNTIME_EXCLUSION_PATHS } from "./git-service.js";
+import { MergeConflictError, createDraftPR, readIntegrationBranch, RUNTIME_EXCLUSION_PATHS } from "./git-service.js";
+import { buildPrEvidence } from "./pr-evidence.js";
 import { debugLog } from "./debug-logger.js";
 import { logWarning, logError } from "./workflow-logger.js";
 import { loadEffectiveGSDPreferences } from "./preferences.js";
@@ -266,6 +270,40 @@ function getActiveWorkspace(): GsdWorkspace | null {
   return activeWorkspace;
 }
 
+function gitPathspecForWorktreePath(basePath: string, targetPath: string): string | null {
+  let base = basePath;
+  let target = targetPath;
+  try {
+    base = realpathSync.native(basePath);
+  } catch {
+    /* keep original */
+    void base;
+  }
+  try {
+    target = realpathSync.native(targetPath);
+  } catch {
+    /* keep original */
+    void target;
+  }
+
+  const rel = relative(base, target);
+  if (rel === "" || rel.startsWith("..") || isAbsolute(rel)) return null;
+  return rel.replaceAll("\\", "/");
+}
+
+function gitRemoteExists(basePath: string, remote: string): boolean {
+  try {
+    execFileSync("git", ["remote", "get-url", remote], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+    });
+    return true;
+  } catch {
+    return false;
+  }
+}
+
 function clearProjectRootStateFiles(basePath: string, milestoneId: string): void {
   const gsdDir = gsdRoot(basePath);
   // Phase C pt 2: auto.lock removed from this list — the file is gone
@@ -301,11 +339,14 @@ function clearProjectRootStateFiles(basePath: string, milestoneId: string): void
   for (const dir of syncedDirs) {
     try {
       if (existsSync(dir)) {
+        const pathspec = gitPathspecForWorktreePath(basePath, dir);
+        if (!pathspec) continue;
+
         // Only remove files that are untracked by git — tracked files are
         // managed by the branch checkout and should not be deleted.
         const untrackedOutput = execFileSync(
           "git",
-          ["ls-files", "--others", "--exclude-standard", dir],
+          ["ls-files", "--others", "--exclude-standard", pathspec],
           { cwd: basePath, stdio: ["ignore", "pipe", "pipe"], encoding: "utf-8" },
         ).trim();
         if (untrackedOutput) {
@@ -2187,16 +2228,18 @@ export function mergeMilestoneToMain(
   let pushed = false;
   if (prefs.auto_push === true && prefs.auto_pr !== true && !nothingToCommit) {
     const remote = prefs.remote ?? "origin";
-    try {
-      execFileSync("git", ["push", remote, mainBranch], {
-        cwd: originalBasePath_,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-      });
-      pushed = true;
-    } catch (err) {
-      // Push failure is non-fatal
-      logWarning("worktree", `git push failed: ${err instanceof Error ? err.message : String(err)}`);
+    if (gitRemoteExists(originalBasePath_, remote)) {
+      try {
+        execFileSync("git", ["push", remote, mainBranch], {
+          cwd: originalBasePath_,
+          stdio: ["ignore", "pipe", "pipe"],
+          encoding: "utf-8",
+        });
+        pushed = true;
+      } catch (err) {
+        // Push failure is non-fatal
+        logWarning("worktree", `git push failed: ${err instanceof Error ? err.message : String(err)}`);
+      }
     }
   }
 
@@ -2205,29 +2248,35 @@ export function mergeMilestoneToMain(
   if (prefs.auto_pr === true && !nothingToCommit) {
     const remote = prefs.remote ?? "origin";
     const prTarget = prefs.pr_target_branch ?? mainBranch;
-    try {
-      // Push the milestone branch to remote first
-      execFileSync("git", ["push", remote, milestoneBranch], {
-        cwd: originalBasePath_,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-      });
-      // Create PR via gh CLI with explicit --head and --base (#2302)
-      execFileSync("gh", [
-        "pr", "create", "--draft",
-        "--base", prTarget,
-        "--head", milestoneBranch,
-        "--title", `Milestone ${milestoneId} complete`,
-        "--body", "Auto-created by GSD on milestone completion.",
-      ], {
-        cwd: originalBasePath_,
-        stdio: ["ignore", "pipe", "pipe"],
-        encoding: "utf-8",
-      });
-      prCreated = true;
-    } catch (err) {
-      // PR creation failure is non-fatal — gh may not be installed or authenticated
-      logWarning("worktree", `PR creation failed: ${err instanceof Error ? err.message : String(err)}`);
+    if (gitRemoteExists(originalBasePath_, remote)) {
+      try {
+        // Push the milestone branch to remote first
+        execFileSync("git", ["push", remote, milestoneBranch], {
+          cwd: originalBasePath_,
+          stdio: ["ignore", "pipe", "pipe"],
+          encoding: "utf-8",
+        });
+        const prEvidence = buildPrEvidence({
+          milestoneId,
+          milestoneTitle,
+          changeType: "feat",
+          summaries: completedSlices.map((slice) => `### ${slice.id}\n${slice.title}`),
+          testsRun: ["Auto-created after milestone merge. Run `npm run verify:pr` before marking this draft ready."],
+          rollbackNotes: ["Close the draft PR or revert the merge commit if review finds a behavior regression."],
+          how: "Generated by git.auto_pr after the milestone branch was pushed and merged locally.",
+        });
+        const prUrl = createDraftPR(originalBasePath_, milestoneId, prEvidence.title, prEvidence.body, {
+          head: milestoneBranch,
+          base: prTarget,
+        });
+        if (!prUrl) {
+          throw new Error("gh pr create returned no URL");
+        }
+        prCreated = true;
+      } catch (err) {
+        // PR creation failure is non-fatal — gh may not be installed or authenticated
+        logWarning("worktree", `PR creation failed: ${err instanceof Error ? err.message : String(err)}`);
+      }
     }
   }
 

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

@@ -147,6 +147,7 @@ import {
   MergeConflictError,
   parseSliceBranch,
   setActiveMilestoneId,
+  resolveProjectRoot,
 } from "./worktree.js";
 import { GitServiceImpl } from "./git-service.js";
 import { getPriorSliceCompletionBlocker } from "./dispatch-guard.js";
@@ -231,6 +232,8 @@ import type { ErrorContext } from "./auto/types.js";
 import { runAutoLoopWithUok } from "./uok/kernel.js";
 import { resolveUokFlags } from "./uok/flags.js";
 import { validateDirectory } from "./validate-directory.js";
+import { createAutoOrchestrator } from "./auto/orchestrator.js";
+import type { AutoOrchestrationModule, AutoOrchestratorDeps } from "./auto/contracts.js";
 // Slice-level parallelism (#2340)
 import { getEligibleSlices } from "./slice-parallel-eligibility.js";
 import { startSliceParallel } from "./slice-parallel-orchestrator.js";
@@ -417,6 +420,17 @@ export function _synthesizePausedSessionRecoveryForTest(
   return synthesizePausedSessionRecovery(basePath, unitType, unitId, sessionFile);
 }
 
+const DETACHED_AUTO_KEEPALIVE_INTERVAL_MS = 30_000;
+
+function withDetachedAutoKeepalive<T>(run: Promise<T>): Promise<T> {
+  const keepAlive = setInterval(() => {}, DETACHED_AUTO_KEEPALIVE_INTERVAL_MS);
+  return run.finally(() => {
+    clearInterval(keepAlive);
+  });
+}
+
+export const _withDetachedAutoKeepaliveForTest = withDetachedAutoKeepalive;
+
 export function startAutoDetached(
   ctx: ExtensionCommandContext,
   pi: ExtensionAPI,
@@ -428,7 +442,7 @@ export function startAutoDetached(
     milestoneLock?: string | null;
   },
 ): void {
-  void startAuto(ctx, pi, base, verboseMode, options).catch((err) => {
+  void withDetachedAutoKeepalive(startAuto(ctx, pi, base, verboseMode, options)).catch((err) => {
     const message = getErrorMessage(err);
     ctx.ui.notify(`Auto-start failed: ${message}`, "error");
     logWarning("engine", `auto start error: ${message}`, { file: "auto.ts" });
@@ -1208,6 +1222,12 @@ export async function stopAuto(
     // changes the user made between sessions (#4959 / CodeRabbit).
     if (pi) clearToolBaseline(pi);
 
+    try {
+      await s.orchestration?.stop(reason ?? "stop");
+    } catch (err) {
+      debugLog("stop-orchestration-stop", { error: err instanceof Error ? err.message : String(err) });
+    }
+
     // Reset all session state in one call
     s.reset();
   }
@@ -1264,6 +1284,7 @@ export async function pauseAuto(
       activeRunDir: s.activeRunDir,
       autoStartTime: s.autoStartTime,
       milestoneLock: s.sessionMilestoneLock ?? undefined,
+      pauseReason: _errorContext?.message,
     };
     setRuntimeKv("global", "", PAUSED_SESSION_KV_KEY, pausedMeta);
   } catch (err) {
@@ -1306,6 +1327,12 @@ export async function pauseAuto(
   resolveAgentEnd({ messages: [] });
   _resetPendingResolve();
 
+  try {
+    await s.orchestration?.stop("pause");
+  } catch (err) {
+    debugLog("pause-orchestration-stop", { error: err instanceof Error ? err.message : String(err) });
+  }
+
   s.active = false;
   s.paused = true;
   deactivateGSD();
@@ -1363,6 +1390,141 @@ function buildResolver(): WorktreeResolver {
   return new WorktreeResolver(s, buildResolverDeps());
 }
 
+/**
+ * Thin entry glue for the new Auto Orchestration module.
+ *
+ * This intentionally wires only dispatch + error notification today, with
+ * no behavior changes to the existing auto loop. It provides a concrete seam
+ * the next refactor steps can adopt incrementally.
+ */
+export function createWiredAutoOrchestrationModule(
+  ctx: ExtensionContext,
+  _pi: ExtensionAPI,
+  dispatchBasePath: string,
+  runtimeBasePath = resolveProjectRoot(dispatchBasePath),
+): AutoOrchestrationModule {
+  const flowId = `auto-orchestrator-${Date.now()}`;
+  let seq = 0;
+
+  const deps: AutoOrchestratorDeps = {
+    dispatch: {
+      async decideNextUnit() {
+        const state = await deriveState(dispatchBasePath);
+        const active = state.activeMilestone;
+        if (!active) return null;
+
+        const prefs = loadEffectiveGSDPreferences(dispatchBasePath)?.preferences;
+        const action = await resolveDispatch({
+          basePath: dispatchBasePath,
+          mid: active.id,
+          midTitle: active.title,
+          state,
+          prefs,
+        });
+
+        if (action.action !== "dispatch") return null;
+        return {
+          unitType: action.unitType,
+          unitId: action.unitId,
+          reason: action.matchedRule ?? "dispatch",
+          preconditions: [],
+        };
+      },
+    },
+    recovery: {
+      async classifyAndRecover(input) {
+        const reason = input.error instanceof Error ? input.error.message : String(input.error ?? "unknown auto error");
+        return { action: "escalate" as const, reason };
+      },
+    },
+    worktree: {
+      async prepareForUnit() {},
+      async syncAfterUnit() {},
+      async cleanupOnStop() {},
+    },
+    health: {
+      async preAdvanceGate() {
+        const gate = await preDispatchHealthGate(dispatchBasePath);
+        return {
+          allow: gate.proceed,
+          reason: gate.reason,
+        };
+      },
+      async postAdvanceRecord(result) {
+        if (result.kind === "error") {
+          recordHealthSnapshot(1, 0, 0, [{
+            code: "orchestration-error",
+            message: result.reason ?? "orchestration error",
+            severity: "error",
+            unitId: "orchestration",
+          }], [], "orchestration");
+        } else if (result.kind === "blocked") {
+          recordHealthSnapshot(0, 1, 0, [{
+            code: "orchestration-blocked",
+            message: result.reason ?? "orchestration blocked",
+            severity: "warning",
+            unitId: "orchestration",
+          }], [], "orchestration");
+        }
+      },
+    },
+    runtime: {
+      async ensureLockOwnership() {
+        const status = getSessionLockStatus(runtimeBasePath);
+        if (!status.valid || status.failureReason === "pid-mismatch") {
+          throw new Error("session lock held by another process");
+        }
+      },
+      async journalTransition(event) {
+        const eventType = event.name === "start"
+          ? "iteration-start"
+          : event.name === "resume"
+            ? "iteration-start"
+            : event.name === "advance"
+              ? "dispatch-match"
+              : event.name === "advance-blocked"
+                ? "guard-block"
+                : event.name === "advance-stopped"
+                  ? "dispatch-stop"
+                  : event.name === "advance-error"
+                    ? "iteration-end"
+                    : event.name === "advance-paused" || event.name === "advance-retry"
+                      ? "guard-block"
+                      : event.name === "stop"
+                      ? "terminal"
+                      : "iteration-end";
+
+        _emitJournalEvent(runtimeBasePath, {
+          ts: new Date().toISOString(),
+          flowId,
+          seq: ++seq,
+          eventType,
+          data: {
+            source: "auto-orchestrator",
+            name: event.name,
+            reason: event.reason,
+            unitType: event.unitType,
+            unitId: event.unitId,
+          },
+        });
+      },
+    },
+    notifications: {
+      async notifyLifecycle(event) {
+        if (event.name === "error") {
+          ctx.ui.notify(event.detail ?? "auto orchestration error", "error");
+        }
+      },
+    },
+  };
+
+  return createAutoOrchestrator(deps);
+}
+
+function ensureOrchestrationModule(ctx: ExtensionContext, pi: ExtensionAPI, basePath: string): void {
+  s.orchestration = createWiredAutoOrchestrationModule(ctx, pi, basePath, lockBase());
+}
+
 /**
  * Build the LoopDeps object from auto.ts private scope.
  * This bundles all private functions that autoLoop needs without exporting them.
@@ -1785,6 +1947,7 @@ export async function startAuto(
       rebuildScope(s.basePath, s.currentMilestoneId);
     }
 
+    ensureOrchestrationModule(ctx, pi, s.basePath || base);
     registerSigtermHandler(lockBase());
 
     ctx.ui.setStatus("gsd-auto", s.stepMode ? "next" : "auto");
@@ -1868,6 +2031,11 @@ export async function startAuto(
     }
     pi.events.emit(CMUX_CHANNELS.LOG, { preferences: loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, message: s.stepMode ? "Step-mode resumed." : "Auto-mode resumed.", level: "progress" });
 
+    try {
+      await s.orchestration?.resume();
+    } catch (err) {
+      debugLog("resume-orchestration-resume", { error: err instanceof Error ? err.message : String(err) });
+    }
     startAutoCommandPolling(s.basePath);
     await runAutoLoopWithUok({
       ctx,
@@ -1904,7 +2072,7 @@ export async function startAuto(
   // Build scope after bootstrap has populated s.basePath / s.originalBasePath /
   // s.currentMilestoneId (including worktree setup inside bootstrapAutoSession).
   rebuildScope(s.basePath, s.currentMilestoneId);
-
+  ensureOrchestrationModule(ctx, pi, s.basePath || base);
   captureProjectRootEnv(s.originalBasePath || s.basePath);
   registerAutoWorkerForSession(s);
   try {
@@ -1915,6 +2083,12 @@ export async function startAuto(
   }
   pi.events.emit(CMUX_CHANNELS.LOG, { preferences: loadEffectiveGSDPreferences(s.basePath || undefined)?.preferences, message: requestedStepMode ? "Step-mode started." : "Auto-mode started.", level: "progress" });
 
+  try {
+    await s.orchestration?.start({ basePath: s.basePath, trigger: "auto-loop" });
+  } catch (err) {
+    debugLog("start-orchestration-start", { error: err instanceof Error ? err.message : String(err) });
+  }
+
   startAutoCommandPolling(s.basePath);
 
   // Dispatch the first unit
@@ -2037,6 +2211,9 @@ export async function dispatchHookUnit(
   }
 
   s.basePath = targetBasePath;
+  if (!s.orchestration) {
+    ensureOrchestrationModule(ctx, pi, s.basePath);
+  }
 
   const hookUnitType = `hook/${hookName}`;
   const hookStartedAt = Date.now();

package/src/resources/extensions/gsd/bootstrap/agent-end-recovery.ts

@@ -1,3 +1,5 @@
+// GSD-2 + src/resources/extensions/gsd/bootstrap/agent-end-recovery.ts - Handles provider and agent-end recovery for GSD auto-mode.
+
 import type { ExtensionAPI, ExtensionContext } from "@gsd/pi-coding-agent";
 
 import { logWarning } from "../workflow-logger.js";
@@ -12,7 +14,7 @@ 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/resolve.js";
+import { isSessionSwitchInFlight, resolveAgentEnd, resolveAgentEndCancelled } from "../auto/resolve.js";
 import { resolveModelId } from "../auto-model-selection.js";
 import { resolveProjectRoot } from "../worktree.js";
 import { clearDiscussionFlowState } from "./write-gate.js";
@@ -56,6 +58,24 @@ function resolveAgentEndBasePath(): string | undefined {
   }
 }
 
+export function _buildAbortedPauseContext(lastMsg: { errorMessage?: unknown }): {
+  message: string;
+  category: "aborted";
+  isTransient: true;
+} {
+  const hasErrorMessage = Object.prototype.hasOwnProperty.call(lastMsg, "errorMessage") && !!lastMsg.errorMessage;
+  return {
+    message: hasErrorMessage ? String(lastMsg.errorMessage) : "Operation aborted",
+    category: "aborted",
+    isTransient: true,
+  };
+}
+
+export function isUserInitiatedAbortMessage(message: string | undefined | null): boolean {
+  if (!message) return false;
+  return /\b(?:claude code process aborted by user|request aborted by user|process aborted by user)\b/i.test(message);
+}
+
 async function pauseTransientWithBackoff(
   cls: ErrorClass,
   pi: ExtensionAPI,
@@ -159,7 +179,7 @@ export async function handleAgentEnd(
       return;
     }
 
-    await pauseAuto(ctx, pi);
+    await pauseAuto(ctx, pi, _buildAbortedPauseContext(lastMsg as { errorMessage?: unknown }));
     return;
   }
   if (lastMsg && "stopReason" in lastMsg && lastMsg.stopReason === "error") {
@@ -167,6 +187,14 @@ export async function handleAgentEnd(
     // is in the assistant message text content. Fall back to content when
     // errorMessage looks uninformative.
     const rawErrorMsg = ("errorMessage" in lastMsg && lastMsg.errorMessage) ? String(lastMsg.errorMessage) : "";
+    if (isUserInitiatedAbortMessage(rawErrorMsg)) {
+      resolveAgentEndCancelled({
+        message: rawErrorMsg,
+        category: "aborted",
+        isTransient: false,
+      });
+      return;
+    }
     const isUseless = !rawErrorMsg || /^(success|ok|true|error|unknown)$/i.test(rawErrorMsg.trim());
     // #3588: When errorMessage is uninformative, extract the real error from
     // the assistant message text content for display purposes only.

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

@@ -1,3 +1,5 @@
+// Project/App: GSD-2
+// File Purpose: Registers DB-backed GSD workflow tools and compatibility aliases.
 import { Type } from "@sinclair/typebox";
 import type { ExtensionAPI } from "@gsd/pi-coding-agent";
 import { Text } from "@gsd/pi-tui";
@@ -8,6 +10,7 @@ import { loadWriteGateSnapshot, shouldBlockRootArtifactSaveInSnapshot } from "./
 import { StringEnum } from "@gsd/pi-ai";
 import { logError } from "../workflow-logger.js";
 import { getErrorMessage } from "../error-utils.js";
+import { incrementLegacyTelemetry } from "../legacy-telemetry.js";
 
 async function loadWorkflowExecutors(): Promise<typeof import("../tools/workflow-tool-executors.js")> {
   return import("../tools/workflow-tool-executors.js");
@@ -19,11 +22,19 @@ async function loadWorkflowExecutors(): Promise<typeof import("../tools/workflow
  */
 // eslint-disable-next-line @typescript-eslint/no-explicit-any -- toolDef shape matches ToolDefinition but typing it fully requires generics
 function registerAlias(pi: ExtensionAPI, toolDef: any, aliasName: string, canonicalName: string): void {
+  const execute = typeof toolDef.execute === "function"
+    ? async (...args: any[]) => {
+        incrementLegacyTelemetry("legacy.mcpAliasUsed");
+        return toolDef.execute(...args);
+      }
+    : toolDef.execute;
+
   pi.registerTool({
     ...toolDef,
     name: aliasName,
     description: toolDef.description + ` (alias for ${canonicalName} — prefer the canonical name)`,
     promptGuidelines: [`Alias for ${canonicalName} — prefer the canonical name.`],
+    execute,
   });
 }
 

package/src/resources/extensions/gsd/bootstrap/register-hooks.ts

@@ -7,7 +7,7 @@ import type { GSDEcosystemBeforeAgentStartHandler } from "../ecosystem/gsd-exten
 import { updateSnapshot } from "../ecosystem/gsd-extension-api.js";
 
 import { buildMilestoneFileName, resolveMilestonePath, resolveSliceFile, resolveSlicePath } from "../paths.js";
-import { canonicalToolName, clearDiscussionFlowState, isDepthConfirmationAnswer, isQueuePhaseActive, markApprovalGateVerified, markDepthVerified, resetWriteGateState, shouldBlockContextWrite, shouldBlockPlanningUnit, shouldBlockQueueExecution, isGateQuestionId, setPendingGate, clearPendingGate, getPendingGate, shouldBlockPendingGate, shouldBlockPendingGateBash, extractDepthVerificationMilestoneId } from "./write-gate.js";
+import { canonicalToolName, clearDiscussionFlowState, isDepthConfirmationAnswer, isQueuePhaseActive, markApprovalGateVerified, markDepthVerified, resetWriteGateState, shouldBlockContextWrite, shouldBlockPlanningUnit, shouldBlockQueueExecution, shouldBlockWorktreeWrite, isGateQuestionId, setPendingGate, clearPendingGate, getPendingGate, shouldBlockPendingGate, shouldBlockPendingGateBash, extractDepthVerificationMilestoneId } from "./write-gate.js";
 import { resolveManifest } from "../unit-context-manifest.js";
 import { isBlockedStateFile, isBashWriteToStateFile, BLOCKED_WRITE_ERROR } from "../write-intercept.js";
 import { loadFile, saveFile, formatContinue } from "../files.js";
@@ -22,6 +22,7 @@ import { logWarning as safetyLogWarning } from "../workflow-logger.js";
 import { installNotifyInterceptor } from "./notify-interceptor.js";
 import { initNotificationStore } from "../notification-store.js";
 import { initNotificationWidget } from "../notification-widget.js";
+import { resolveWorktreeProjectRoot } from "../worktree-root.js";
 import { extractSubagentAgentClasses } from "./subagent-input.js";
 import { approvalGateIdForUnit, isExplicitApprovalResponse, shouldPauseForUserApprovalQuestion } from "../user-input-boundary.js";
 
@@ -64,6 +65,16 @@ async function applyDisabledModelProviderPolicy(ctx: ExtensionContext): Promise<
   }
 }
 
+export function resolveNotificationStoreBasePath(cwd: string = process.cwd()): string {
+  return resolveWorktreeProjectRoot(cwd);
+}
+
+function initSessionNotifications(ctx: ExtensionContext): void {
+  initNotificationStore(resolveNotificationStoreBasePath());
+  installNotifyInterceptor(ctx);
+  initNotificationWidget(ctx);
+}
+
 async function writeContextModeCompactionSnapshot(basePath: string): Promise<void> {
   try {
     const { loadEffectiveGSDPreferences } = await import("../preferences.js");
@@ -101,9 +112,7 @@ export function registerHooks(
   ecosystemHandlers: GSDEcosystemBeforeAgentStartHandler[],
 ): void {
   pi.on("session_start", async (_event, ctx) => {
-    initNotificationStore(process.cwd());
-    installNotifyInterceptor(ctx);
-    initNotificationWidget(ctx);
+    initSessionNotifications(ctx);
     if (!isAutoActive()) {
       const { initHealthWidget } = await import("../health-widget.js");
       initHealthWidget(ctx);
@@ -156,8 +165,7 @@ export function registerHooks(
   });
 
   pi.on("session_switch", async (_event, ctx) => {
-    initNotificationStore(process.cwd());
-    installNotifyInterceptor(ctx);
+    initSessionNotifications(ctx);
     resetWriteGateState(process.cwd());
     resetToolCallLoopGuard();
     await resetAskUserQuestionsTurnCache();
@@ -474,6 +482,22 @@ export function registerHooks(
       }
     }
 
+    // ── Worktree-isolation write gate (#5199) ────────────────────────────
+    // Block planning-write tools from landing code at the project root when
+    // git.isolation=worktree but auto-mode hasn't created the milestone
+    // worktree yet. Without this, writes silently orphan outside git history.
+    if (isToolCallEventType("write", event) || isToolCallEventType("edit", event)) {
+      const wtBasePath = resolveWorktreeProjectRoot(dash.basePath ?? discussionBasePath);
+      const wtGuard = shouldBlockWorktreeWrite(
+        event.toolName,
+        event.input.path,
+        wtBasePath,
+        isAutoActive(),
+        dash.currentUnit?.type,
+      );
+      if (wtGuard.block) return wtGuard;
+    }
+
     // ── Single-writer engine: block direct writes to STATE.md ──────────
     // Covers write, edit, and bash tools to prevent bypass vectors.
     if (isToolCallEventType("write", event)) {