gsd-pi 2.82.0-dev.2841a1e44 → 2.82.0-dev.9d5798940

package/src/resources/extensions/gsd/auto-post-unit.ts

@@ -41,6 +41,7 @@ import {
   resolveExpectedArtifactPath,
   writeBlockerPlaceholder,
   diagnoseExpectedArtifact,
+  diagnoseWorktreeIntegrityFailure,
 } from "./auto-recovery.js";
 import { regenerateIfMissing } from "./workflow-projections.js";
 import { WorktreeStateProjection } from "./worktree-state-projection.js";
@@ -381,6 +382,23 @@ export function buildStepCompleteMessage(nextState: import("./types.js").GSDStat
     + `Run /clear, then /gsd to continue (or /gsd auto to run continuously).`;
 }
 
+/**
+ * Decide whether step mode should stop at the step wizard after a unit finishes.
+ *
+ * @param currentUnitType The just-finished unit type, such as "execute-task" or
+ *   "complete-milestone"; may be null/undefined when no current unit is known.
+ * @param phaseAfterUnit The freshly derived next phase, such as "executing" or
+ *   "complete"; may be null/undefined if state derivation failed.
+ * @returns true to show the step wizard; false to keep the loop running so
+ *   terminal milestone completion can reach the merge/finalization path.
+ */
+export function shouldReturnStepWizardAfterUnit(
+  currentUnitType: string | null | undefined,
+  phaseAfterUnit: string | null | undefined,
+): boolean {
+  return currentUnitType !== "complete-milestone" && phaseAfterUnit !== "complete";
+}
+
 export interface PreVerificationOpts {
   skipSettleDelay?: boolean;
   skipWorktreeSync?: boolean;
@@ -413,6 +431,11 @@ function artifactValidationKind(unitType: string): "project" | "requirements" |
 }
 
 function describeArtifactVerificationFailure(unitType: string, unitId: string, basePath: string): string {
+  const worktreeFailure = diagnoseWorktreeIntegrityFailure(basePath);
+  if (worktreeFailure) {
+    return `${worktreeFailure} Unit: ${unitType} ${unitId}.`;
+  }
+
   const artifactPath = resolveExpectedArtifactPath(unitType, unitId, basePath);
   if (!artifactPath) {
     return `Artifact verification failed: ${unitType} "${unitId}" has no resolvable artifact path.`;
@@ -469,9 +492,17 @@ export async function autoCommitUnit(
   }
 }
 
+/**
+ * Execute the turn-level git action (commit, snapshot, or status-only).
+ *
+ * @param opts.softFailure - Defaults to false. When true, retry git failures,
+ * warn, and continue without pausing auto-mode; use for best-effort deferred
+ * closeout work where a git failure should not block the run.
+ */
 async function runCloseoutGitAction(
   pctx: PostUnitContext,
   unit: NonNullable<AutoSession["currentUnit"]>,
+  opts?: { softFailure?: boolean },
 ): Promise<"continue" | "dispatched"> {
   const { s, ctx, pi, pauseAuto } = pctx;
   const prefs = loadEffectiveGSDPreferences()?.preferences;
@@ -506,13 +537,24 @@ async function runCloseoutGitAction(
         unitId: unit.id,
       });
     } else {
-      const gitResult = runTurnGitAction({
+      const maxAttempts = opts?.softFailure ? 3 : 1;
+      let gitResult = runTurnGitAction({
         basePath: s.basePath,
         action: turnAction,
         unitType: unit.type,
         unitId: unit.id,
         taskContext,
       });
+      for (let attempt = 1; gitResult.status === "failed" && attempt < maxAttempts; attempt++) {
+        await new Promise((resolve) => setTimeout(resolve, 250 * attempt));
+        gitResult = runTurnGitAction({
+          basePath: s.basePath,
+          action: turnAction,
+          unitType: unit.type,
+          unitId: unit.id,
+          taskContext,
+        });
+      }
 
       if (uokFlags.gitops) {
         writeTurnGitTransaction({
@@ -563,12 +605,15 @@ async function runCloseoutGitAction(
         }
 
         const failureMsg = `Git ${turnAction} failed: ${(gitResult.error ?? "unknown error").split("\n")[0]}`;
-        ctx.ui.notify(failureMsg, "error");
+        ctx.ui.notify(failureMsg, opts?.softFailure ? "warning" : "error");
         debugLog("postUnit", {
-          phase: "git-action-failed-blocking",
+          phase: opts?.softFailure ? "git-action-failed-soft" : "git-action-failed-blocking",
           action: turnAction,
           error: gitResult.error ?? "unknown error",
         });
+        if (opts?.softFailure) {
+          return "continue";
+        }
         await pauseAuto(ctx, pi);
         return "dispatched";
       }
@@ -586,7 +631,10 @@ async function runCloseoutGitAction(
     s.lastGitActionFailure = message;
     s.lastGitActionStatus = "failed";
     debugLog("postUnit", { phase: "git-action", error: message, action: turnAction });
-    ctx.ui.notify(`Git ${turnAction} failed: ${message.split("\n")[0]}`, uokFlags.gitops ? "error" : "warning");
+    ctx.ui.notify(`Git ${turnAction} failed: ${message.split("\n")[0]}`, opts?.softFailure ? "warning" : "error");
+    if (opts?.softFailure) {
+      return "continue";
+    }
     if (uokFlags.gitops) {
       await pauseAuto(ctx, pi);
       return "dispatched";
@@ -1133,6 +1181,24 @@ export async function postUnitPreVerification(pctx: PostUnitContext, opts?: PreV
           "warning",
         );
         // Fall through to "continue" — do NOT enter the retry or db-unavailable paths.
+      } else if (!triggerArtifactVerified && diagnoseWorktreeIntegrityFailure(s.basePath)) {
+        const retryKey = `${s.currentUnit.type}:${s.currentUnit.id}`;
+        const worktreeFailure = diagnoseWorktreeIntegrityFailure(s.basePath)!;
+        s.pendingVerificationRetry = null;
+        s.verificationRetryCount.delete(retryKey);
+        s.verificationRetryFailureHashes.delete(retryKey);
+        debugLog("postUnit", {
+          phase: "worktree-integrity-failure",
+          unitType: s.currentUnit.type,
+          unitId: s.currentUnit.id,
+          basePath: s.basePath,
+        });
+        ctx.ui.notify(
+          `${worktreeFailure} Retry ${s.currentUnit.id} after repair.`,
+          "error",
+        );
+        await pauseAuto(ctx, pi);
+        return "dispatched";
       } else if (!triggerArtifactVerified && !isDbAvailable()) {
         debugLog("postUnit", { phase: "artifact-verify-skip-db-unavailable", unitType: s.currentUnit.type, unitId: s.currentUnit.id });
         const dbSkipDiag = diagnoseExpectedArtifact(s.currentUnit.type, s.currentUnit.id, s.basePath);
@@ -1220,7 +1286,7 @@ export async function postUnitPostVerification(pctx: PostUnitContext): Promise<"
 
   if (s.currentUnit) {
     if (shouldDeferCloseoutGitAction(s.currentUnit.type)) {
-      const gitActionResult = await runCloseoutGitAction(pctx, s.currentUnit);
+      const gitActionResult = await runCloseoutGitAction(pctx, s.currentUnit, { softFailure: true });
       if (gitActionResult === "dispatched") {
         return "stopped";
       }
@@ -1668,14 +1734,18 @@ export async function postUnitPostVerification(pctx: PostUnitContext): Promise<"
   // Without this notify(), /gsd in step mode finishes a unit and silently
   // exits the loop, leaving the user with no hint to /clear and /gsd again.
   if (s.stepMode) {
+    let phaseAfterUnit: string | null = null;
     try {
       const nextState = await deriveState(s.canonicalProjectRoot);
+      phaseAfterUnit = nextState.phase;
       ctx.ui.notify(buildStepCompleteMessage(nextState), "info");
     } catch (e) {
       debugLog("postUnit", { phase: "step-wizard-notify", error: String(e) });
       ctx.ui.notify(STEP_COMPLETE_FALLBACK_MESSAGE, "info");
     }
-    return "step-wizard";
+    return shouldReturnStepWizardAfterUnit(s.currentUnit?.type, phaseAfterUnit)
+      ? "step-wizard"
+      : "continue";
   }
 
   return "continue";

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

@@ -46,6 +46,7 @@ import {
 import { classifyMilestoneSummaryContent } from "./milestone-summary-classifier.js";
 import { validateArtifact } from "./schemas/validate.js";
 import { getProjectResearchStatus } from "./project-research-policy.js";
+import { isGsdWorktreePath } from "./worktree-root.js";
 
 // Re-export so existing consumers of auto-recovery.ts keep working.
 export { resolveExpectedArtifactPath, diagnoseExpectedArtifact };
@@ -56,6 +57,29 @@ export {
 
 // ─── Artifact Resolution & Verification ───────────────────────────────────────
 
+export function diagnoseWorktreeIntegrityFailure(basePath: string): string | null {
+  if (!isGsdWorktreePath(basePath)) return null;
+  if (!existsSync(basePath)) {
+    return `Worktree integrity failure: ${basePath} does not exist. Repair or recreate the worktree before retrying.`;
+  }
+
+  const gitPath = join(basePath, ".git");
+  if (!existsSync(gitPath)) {
+    return `Worktree integrity failure: ${basePath} is not a valid git worktree (.git missing). Repair or recreate the worktree before retrying.`;
+  }
+
+  try {
+    execFileSync("git", ["rev-parse", "--git-dir"], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+    });
+    return null;
+  } catch (err) {
+    return `Worktree integrity failure: ${basePath} is not a valid git worktree (git rev-parse failed: ${getErrorMessage(err).split("\n")[0]}). Repair or recreate the worktree before retrying.`;
+  }
+}
+
 export type ArtifactRecoveryDbRefreshResult =
   | { ok: true }
   | { ok: false; fatal: boolean; message: string; reason: string };
@@ -752,6 +776,11 @@ export function verifyExpectedArtifact(
     return false;
   }
   if (!existsSync(absPath)) {
+    const worktreeFailure = diagnoseWorktreeIntegrityFailure(base);
+    if (worktreeFailure) {
+      logError("recovery", `${worktreeFailure} Unit: ${unitType} ${unitId}.`);
+      return false;
+    }
     logWarning("recovery", `verify-fail ${unitType} ${unitId}: existsSync false for ${absPath}`);
     return false;
   }

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

@@ -818,14 +818,18 @@ export async function bootstrapAutoSession(
     // worktree cleanup) was never run — the survivor branch must be merged.
     // Applies to both worktree and branch isolation modes.
     let hasSurvivorBranch = false;
+    let survivorMilestoneId = state.activeMilestone?.id ?? null;
+    if (!survivorMilestoneId && state.phase === "complete") {
+      survivorMilestoneId = findUnmergedCompletedMilestone(base, getIsolationMode(base));
+    }
     if (
-      state.activeMilestone &&
+      survivorMilestoneId &&
       (state.phase === "pre-planning" || state.phase === "complete") &&
       getIsolationMode(base) !== "none" &&
       !detectWorktreeName(base) &&
       !base.includes(`${pathSep}.gsd${pathSep}worktrees${pathSep}`)
     ) {
-      const milestoneBranch = `milestone/${state.activeMilestone.id}`;
+      const milestoneBranch = `milestone/${survivorMilestoneId}`;
       const { nativeBranchExists } = await import("./native-git-bridge.js");
       hasSurvivorBranch = nativeBranchExists(base, milestoneBranch);
       if (hasSurvivorBranch) {
@@ -869,7 +873,7 @@ export async function bootstrapAutoSession(
     // Re-evaluate via the helper — the discuss branch above may have cleared
     // hasSurvivorBranch after a successful promotion.
     if (decideSurvivorAction(hasSurvivorBranch, state.phase) === "finalize") {
-      const mid = state.activeMilestone!.id;
+      const mid = survivorMilestoneId!;
       // Commit 68ef58a3c made `_mergeBranchMode` throw on wrong-branch
       // instead of returning false silently. Wrap the call so the throw is
       // converted into an error notify + clean bootstrap abort, not an

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

@@ -282,6 +282,50 @@ function gitRemoteExists(basePath: string, remote: string): boolean {
   }
 }
 
+function findRegularMergeChangedPaths(basePath: string, milestoneBranch: string, mainBranch: string): Set<string> {
+  const changedPaths = new Set<string>();
+  let mergeLog = "";
+  try {
+    mergeLog = execFileSync("git", ["rev-list", "--merges", "--parents", mainBranch], {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+    }).trim();
+  } catch (err) {
+    logWarning("worktree", `regular merge lookup failed: ${err instanceof Error ? err.message : String(err)}`);
+    return changedPaths;
+  }
+
+  for (const line of mergeLog.split("\n").filter(Boolean)) {
+    const [mergeCommit, firstParent, ...otherParents] = line.split(" ");
+    if (!mergeCommit || !firstParent || otherParents.length === 0) continue;
+    const mergedMilestone = otherParents.some((parent) => {
+      try {
+        return nativeIsAncestor(basePath, milestoneBranch, parent);
+      } catch {
+        return false;
+      }
+    });
+    if (!mergedMilestone) continue;
+
+    try {
+      const output = execFileSync("git", ["diff", "--name-only", firstParent, mergeCommit], {
+        cwd: basePath,
+        stdio: ["ignore", "pipe", "pipe"],
+        encoding: "utf-8",
+      }).trim();
+      for (const path of output.split("\n").filter(Boolean)) {
+        if (!path.startsWith(".gsd/")) changedPaths.add(path);
+      }
+    } catch (err) {
+      logWarning("worktree", `regular merge diff lookup failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    return changedPaths;
+  }
+
+  return changedPaths;
+}
+
 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
@@ -1739,6 +1783,66 @@ export function mergeMilestoneToMain(
     }
   }
 
+  // Already regular-merged milestones can skip the squash path and proceed to cleanup (#5831).
+  if (nativeIsAncestor(originalBasePath_, milestoneBranch, mainBranch)) {
+    const codeChanges = nativeDiffNumstat(
+      originalBasePath_,
+      mainBranch,
+      milestoneBranch,
+    ).filter((entry) => !entry.path.startsWith(".gsd/"));
+    if (codeChanges.length > 0) {
+      const regularMergeChangedPaths = findRegularMergeChangedPaths(
+        originalBasePath_,
+        milestoneBranch,
+        mainBranch,
+      );
+      const unanchoredCodeChanges = codeChanges.filter((entry) =>
+        regularMergeChangedPaths.has(entry.path)
+      );
+      if (unanchoredCodeChanges.length > 0) {
+        process.chdir(previousCwd);
+        throw new GSDError(
+          GSD_GIT_ERROR,
+          `Milestone branch "${milestoneBranch}" is reachable from "${mainBranch}" ` +
+            `but has ${unanchoredCodeChanges.length} milestone-touched code file(s) not on current "${mainBranch}". ` +
+            `Aborting worktree teardown to prevent data loss.`,
+        );
+      }
+    }
+    debugLog("mergeMilestoneToMain", {
+      action: "skip-squash-already-merged",
+      milestoneId,
+      milestoneBranch,
+      mainBranch,
+    });
+    try {
+      clearProjectRootStateFiles(originalBasePath_, milestoneId);
+    } catch (err) {
+      logWarning("worktree", `clearProjectRootStateFiles failed during already-merged cleanup: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    try {
+      removeWorktree(originalBasePath_, milestoneId, {
+        branch: milestoneBranch,
+        deleteBranch: false,
+      });
+    } catch (err) {
+      logWarning("worktree", `worktree removal failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    try {
+      nativeBranchDelete(originalBasePath_, milestoneBranch);
+    } catch (err) {
+      logWarning("worktree", `git branch-delete failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    setActiveWorkspace(null);
+    nudgeGitBranchCache(previousCwd);
+    try {
+      process.chdir(originalBasePath_);
+    } catch (err) {
+      logWarning("worktree", `chdir to project root after already-merged cleanup failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    return { commitMessage, pushed: false, prCreated: false, codeFilesChanged: true };
+  }
+
   // 7. Shelter queued milestone directories before the squash merge (#2505).
   // The milestone branch may contain copies of queued milestone dirs (via
   // copyPlanningArtifacts), so `git merge --squash` rejects when those same

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

@@ -48,6 +48,11 @@ const MAX_NETWORK_RETRIES = 2;
 function isObjectRecord(value: unknown): value is Record<string, unknown> {
   return !!value && typeof value === "object";
 }
+
+export function _hasEmptyAgentEndContent(content: unknown): boolean {
+  return content == null || (Array.isArray(content) && content.length === 0);
+}
+
 /**
  * Cap on auto-resume attempts for sustained transient-provider errors.
  *
@@ -310,7 +315,7 @@ export async function handleAgentEnd(
     // that carry error context — e.g. errorMessage field or non-empty content
     // indicating a mid-stream failure. (#2695)
     const content = "content" in lastMsg ? lastMsg.content : undefined;
-    const hasEmptyContent = Array.isArray(content) && content.length === 0;
+    const hasEmptyContent = _hasEmptyAgentEndContent(content);
     const hasErrorMessage = "errorMessage" in lastMsg && !!lastMsg.errorMessage;
 
     if (hasEmptyContent && !hasErrorMessage) {

package/src/resources/extensions/gsd/bootstrap/write-gate.ts

@@ -65,6 +65,7 @@ const QUEUE_SAFE_TOOLS = new Set([
  *   true / false        — shell no-ops / test exit codes
  */
 const BASH_READ_ONLY_RE = /^\s*(cat|head|tail|less|more|wc|file|stat|du|df|which|type|echo|printf|ls|find|grep|rg|awk|sed\b(?!.*-i)|sort|uniq|diff|comm|tr|cut|tee\s+-a\s+\/dev\/null|git\s+(log|show|diff|status|branch|tag|remote|rev-parse|ls-files|blame|shortlog|describe|stash\s+list|config\s+--get|cat-file)|gh\s+(issue|pr|api|repo|release)\s+(view|list|diff|status|checks)|mkdir\s+-p\s+\.gsd|rtk\s|npm\s+run\s+(test|test:\w+|lint|lint:\w+|typecheck|type-check|type-check:\w+|check|verify|audit|outdated|format:check|ci|validate)\b|npm\s+(ls|list|info|view|show|outdated|audit|explain|doctor|ping|--version|-v)\b|npx\s|tsx\s|node\s+(--print|--version|-v\b)|python[23]?\s+(-c\s+'[^']*'|--version|-V\b|-m\s+(pip\s+show|pip\s+list|site))|pip[23]?\s+(show|list|freeze|check|index\s+versions)\b|jq\s|yq\s|curl\s+(-s\b|--silent\b)(?!\s+[^|>]*\s-[oO]\b)(?!\s+[^|>]*\s--output\b)[^|>]*$|openssl\s+(version|x509|s_client)|env\b|printenv\b|true\b|false\b)/;
+const BASH_VERIFICATION_RE = /^\s*(npm\s+(run\s+(build|test|test:\w+|lint|lint:\w+|typecheck|type-check|verify|ci|validate)\b|test\b)|pnpm\s+(build|test|lint|typecheck|verify)\b|yarn\s+(build|test|lint|typecheck|verify)\b|vitest\b|jest\b|go\s+test\b)/;
 
 interface InMemoryWriteGateState {
   verifiedDepthMilestones: Set<string>;
@@ -767,6 +768,9 @@ function blockReason(unitType: string, mode: string, what: string): string {
  *                    and listed in the policy's allowedSubagents.
  *   - "docs"       → like "planning" but also allows writes to paths
  *                    matching `allowedPathGlobs` relative to basePath.
+ *   - "verification"
+ *                  → allows Bash for project verification commands, but keeps
+ *                    writes restricted to .gsd/ and blocks subagent dispatch.
  *
  * `pathOrCommand` is the file path for write/edit-shaped tools and the
  * shell command for bash. Other tools ignore this argument.
@@ -804,7 +808,7 @@ export function shouldBlockPlanningUnit(
     return { block: true, reason: blockReason(unitType, policy.mode, `tool "${tool}" is not on the read-only allowlist`) };
   }
 
-  // planning / planning-dispatch / docs modes share the same surface for safe tools, bash, and subagent.
+  // planning / planning-dispatch / docs / verification modes share the same surface for safe tools, bash, and subagent.
   if (PLANNING_SAFE_TOOLS.has(tool)) return { block: false };
   if (tool.startsWith("gsd_")) return { block: false };
 
@@ -862,6 +866,17 @@ export function shouldBlockPlanningUnit(
   }
 
   if (tool === "bash") {
+    if (policy.mode === "verification") {
+      if (BASH_VERIFICATION_RE.test(pathOrCommand) || BASH_READ_ONLY_RE.test(pathOrCommand)) return { block: false };
+      return {
+        block: true,
+        reason: blockReason(
+          unitType,
+          policy.mode,
+          `bash is restricted to build/test verification commands (npm run build, npm test, etc.); cannot run "${pathOrCommand.slice(0, 80)}${pathOrCommand.length > 80 ? "…" : ""}"`,
+        ),
+      };
+    }
     if (BASH_READ_ONLY_RE.test(pathOrCommand)) return { block: false };
     return {
       block: true,

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

@@ -1,6 +1,7 @@
 import type { ExtensionAPI, ExtensionCommandContext, ExtensionContext } from "@gsd/pi-coding-agent";
 import type { Model } from "@gsd/pi-ai";
 import type { GSDState } from "../../types.js";
+import { createRequire } from "node:module";
 
 import { computeProgressScore, formatProgressLine } from "../../progress-score.js";
 import { loadEffectiveGSDPreferences, getGlobalGSDPreferencesPath, getProjectGSDPreferencesPath } from "../../preferences.js";
@@ -220,7 +221,22 @@ export async function handleBrief(args: string, ctx: ExtensionCommandContext, pi
   }
 
   const outputDir = getVisualBriefOutputDir();
-  pi.sendUserMessage(buildVisualBriefPrompt(request, { outputDir }));
+  const version = resolveGsdVersion();
+  pi.sendUserMessage(buildVisualBriefPrompt(request, { outputDir, version }));
+}
+
+const briefRequire = createRequire(import.meta.url);
+
+function resolveGsdVersion(): string | undefined {
+  const envVersion = process.env.GSD_VERSION?.trim();
+  if (envVersion) return envVersion;
+  try {
+    const pkg = briefRequire("../../../../../../package.json") as { version?: unknown };
+    const fromPkg = typeof pkg.version === "string" ? pkg.version.trim() : "";
+    return fromPkg || undefined;
+  } catch {
+    return undefined;
+  }
 }
 
 export async function handleSetup(args: string, ctx: ExtensionCommandContext, pi?: ExtensionAPI): Promise<void> {

package/src/resources/extensions/gsd/db/unit-dispatches.ts

@@ -524,7 +524,7 @@ export function getRecentUnitKeysForProjectRoot(
   if (!isDbAvailable()) return [];
   const db = _getAdapter()!;
   const rows = db.prepare(
-    `SELECT ud.unit_id
+    `SELECT ud.unit_type, ud.unit_id
      FROM unit_dispatches ud
      INNER JOIN workers w ON w.worker_id = ud.worker_id
      WHERE w.project_root_realpath = :project_root_realpath
@@ -533,8 +533,8 @@ export function getRecentUnitKeysForProjectRoot(
   ).all({
     ":project_root_realpath": projectRootRealpath,
     ":limit": limit,
-  }) as Array<{ unit_id: string }>;
-  return rows.reverse().map((r) => ({ key: r.unit_id }));
+  }) as Array<{ unit_type: string; unit_id: string }>;
+  return rows.reverse().map((r) => ({ key: `${r.unit_type}/${r.unit_id}` }));
 }
 
 /**