gsd-pi 2.82.0-dev.2841a1e44 → 2.82.0-dev.98ea09b1e

package/src/resources/extensions/gsd/git-service.ts

@@ -270,6 +270,30 @@ function isExcludedScopedPath(path: string, exclusions: readonly string[]): bool
   return false;
 }
 
+function submodulePathsFromLsFiles(output: string): Set<string> {
+  const submodulePaths = new Set<string>();
+  if (!output) return submodulePaths;
+
+  for (const line of output.split("\n")) {
+    const match = line.match(/^160000\s+\S+\s+\d+\t(.+)$/);
+    if (!match) continue;
+    submodulePaths.add(match[1].replace(/\\/g, "/").replace(/\/+$/, ""));
+  }
+  return submodulePaths;
+}
+
+function isInsideSubmodule(path: string, submodulePaths: ReadonlySet<string>): boolean {
+  const normalizedPath = path.replace(/\\/g, "/");
+  if (submodulePaths.has(normalizedPath)) return true;
+
+  let slashIndex = normalizedPath.lastIndexOf("/");
+  while (slashIndex > 0) {
+    if (submodulePaths.has(normalizedPath.slice(0, slashIndex))) return true;
+    slashIndex = normalizedPath.lastIndexOf("/", slashIndex - 1);
+  }
+  return false;
+}
+
 /**
  * Thrown when a slice merge hits code conflicts in non-.gsd files.
  * The working tree is left in a conflicted state (no reset) so the
@@ -764,6 +788,26 @@ export class GitServiceImpl {
       .filter(file => !nativeIsIgnored(this.basePath, file))
       .filter(file => !isExcludedScopedPath(file, allExclusions));
 
+    const scopedPaths: string[] = [];
+    const submodulePaths: string[] = [];
+    const repoSubmodules = submodulePathsFromLsFiles(
+      runGit(this.basePath, ["ls-files", "--stage"], { allowFailure: true }),
+    );
+    for (const path of normalized) {
+      if (isInsideSubmodule(path, repoSubmodules)) {
+        submodulePaths.push(path);
+      } else {
+        scopedPaths.push(path);
+      }
+    }
+    if (submodulePaths.length > 0) {
+      logWarning(
+        "engine",
+        `scoped stage: dropping ${submodulePaths.length} keyFile(s) inside git submodule(s): ${submodulePaths.join(", ")}`,
+        { file: "git-service.ts" },
+      );
+    }
+
     // Drop entries that don't exist on disk. The LLM occasionally lists files
     // it intended to write but didn't (or names them with wrong casing/path).
     // Pre-`b304f738b` `git add -A` swallowed these silently; the scoped
@@ -771,7 +815,7 @@ export class GitServiceImpl {
     // the whole commit fail (see #5500). Filter so valid paths still commit.
     const missing: string[] = [];
     const existing: string[] = [];
-    for (const path of normalized) {
+    for (const path of scopedPaths) {
       if (existsSync(join(this.basePath, path))) {
         existing.push(path);
       } else {

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

@@ -2081,6 +2081,9 @@ export function deleteTask(milestoneId: string, sliceId: string, taskId: string)
     currentDb!.prepare(
       `DELETE FROM verification_evidence WHERE milestone_id = :mid AND slice_id = :sid AND task_id = :tid`,
     ).run({ ":mid": milestoneId, ":sid": sliceId, ":tid": taskId });
+    currentDb!.prepare(
+      `DELETE FROM quality_gates WHERE milestone_id = :mid AND slice_id = :sid AND task_id = :tid`,
+    ).run({ ":mid": milestoneId, ":sid": sliceId, ":tid": taskId });
     currentDb!.prepare(
       `DELETE FROM tasks WHERE milestone_id = :mid AND slice_id = :sid AND id = :tid`,
     ).run({ ":mid": milestoneId, ":sid": sliceId, ":tid": taskId });

package/src/resources/extensions/gsd/guided-flow.ts

@@ -1539,6 +1539,7 @@ export async function showDiscuss(
       const discussMilestoneTemplates = inlineTemplate("context", "Context");
       const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
       const basePrompt = loadPrompt("guided-discuss-milestone", {
+        workingDirectory: basePath,
         milestoneId: mid, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
         commitInstruction: buildDocsCommitInstruction(`docs(${mid}): milestone context from discuss`),
         fastPathInstruction: "",
@@ -1553,6 +1554,7 @@ export async function showDiscuss(
       const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
       setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId: mid, step: false });
       await dispatchWorkflow(pi, loadPrompt("guided-discuss-milestone", {
+        workingDirectory: basePath,
         milestoneId: mid, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
         commitInstruction: buildDocsCommitInstruction(`docs(${mid}): milestone context from discuss`),
         fastPathInstruction: "",
@@ -1822,6 +1824,7 @@ async function dispatchDiscussForMilestone(
   const discussMilestoneTemplates = inlineTemplate("context", "Context");
   const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
   const basePrompt = loadPrompt("guided-discuss-milestone", {
+    workingDirectory: basePath,
     milestoneId: mid,
     milestoneTitle,
     inlinedTemplates: discussMilestoneTemplates,
@@ -2121,18 +2124,19 @@ export async function showSmartEntry(
 
   if (interrupted.classification !== "recoverable") {
     try {
-      const { autoImportMarkdownHierarchyIfDbMismatch } = await import("./migration-auto-check.js");
-      const result = await autoImportMarkdownHierarchyIfDbMismatch(basePath);
-      if (result.action === "imported") {
+      const { checkMarkdownHierarchyAgainstDb } = await import("./migration-auto-check.js");
+      const result = await checkMarkdownHierarchyAgainstDb(basePath);
+      if (result.action === "recovery-required") {
         ctx.ui.notify(
-          `Recovered migrated planning state into gsd.db (${result.reason}): ${result.afterDb.milestones} milestone(s), ${result.afterDb.slices} slice(s), ${result.afterDb.tasks} task(s).`,
-          "info",
+          result.message ??
+            `Markdown planning artifacts do not match the authoritative DB. Run \`${result.recoveryCommand ?? "gsd recover"}\` to import markdown explicitly.`,
+          "warning",
         );
       }
     } catch (err) {
       const message = err instanceof Error ? err.message : String(err);
-      ctx.ui.notify(`GSD could not auto-import existing planning state into gsd.db: ${message}`, "warning");
-      logWarning("guided", `planning state auto-import failed: ${message}`, { file: "guided-flow.ts" });
+      ctx.ui.notify(`GSD could not compare markdown planning artifacts with gsd.db: ${message}`, "warning");
+      logWarning("guided", `planning state DB/markdown comparison failed: ${message}`, { file: "guided-flow.ts" });
     }
   }
 
@@ -2356,6 +2360,7 @@ export async function showSmartEntry(
       const discussMilestoneTemplates = inlineTemplate("context", "Context");
       const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
       const basePrompt = loadPrompt("guided-discuss-milestone", {
+        workingDirectory: basePath,
         milestoneId, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
         commitInstruction: buildDocsCommitInstruction(`docs(${milestoneId}): milestone context from discuss`),
         fastPathInstruction: "",
@@ -2370,6 +2375,7 @@ export async function showSmartEntry(
       const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
       setPendingAutoStart(basePath, { ctx, pi, basePath, milestoneId, step: stepMode });
       await dispatchWorkflow(pi, loadPrompt("guided-discuss-milestone", {
+        workingDirectory: basePath,
         milestoneId, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
         commitInstruction: buildDocsCommitInstruction(`docs(${milestoneId}): milestone context from discuss`),
         fastPathInstruction: "",
@@ -2462,6 +2468,7 @@ export async function showSmartEntry(
         const discussMilestoneTemplates = inlineTemplate("context", "Context");
         const structuredQuestionsAvailable = getStructuredQuestionsAvailability(pi, ctx);
         await dispatchWorkflow(pi, loadPrompt("guided-discuss-milestone", {
+          workingDirectory: basePath,
           milestoneId, milestoneTitle, inlinedTemplates: discussMilestoneTemplates, structuredQuestionsAvailable,
           commitInstruction: buildDocsCommitInstruction(`docs(${milestoneId}): milestone context from discuss`),
           fastPathInstruction: "",

package/src/resources/extensions/gsd/migrate/parsers.ts

@@ -95,6 +95,17 @@ function parsePhaseEntry(line: string): PlanningRoadmapEntry | null {
     };
   }
 
+  // Format 3: - ✅ v1.0 MVP — Phases 1-6
+  const fmtVersionPhases = stripped.match(/^-\s+([✅🚧])\s+v\d+(?:\.\d+)*\s+(.+?)\s*[—–]\s*Phases?\s+(\d+(?:\.\d+)?)(?:\s*-\s*\d+(?:\.\d+)?)?(?:\s+\(.*\))?\s*$/iu);
+  if (fmtVersionPhases) {
+    return {
+      number: parseFloat(fmtVersionPhases[3]),
+      title: fmtVersionPhases[2].trim(),
+      done: fmtVersionPhases[1] === '✅',
+      raw: line,
+    };
+  }
+
   return null;
 }
 

package/src/resources/extensions/gsd/migration-auto-check.ts

@@ -2,21 +2,17 @@ import { existsSync, readdirSync, readFileSync } from "node:fs";
 
 import { ensureDbOpen } from "./bootstrap/dynamic-tools.js";
 import {
-  clearEngineHierarchy,
   getAllMilestones,
   getMilestoneSlices,
   getSliceTasks,
   isDbAvailable,
-  transaction,
 } from "./gsd-db.js";
-import { migrateHierarchyToDb } from "./md-importer.js";
 import { parsePlan, parseRoadmap } from "./parsers-legacy.js";
 import {
   milestonesDir,
   resolveMilestoneFile,
   resolveSliceFile,
 } from "./paths.js";
-import { invalidateStateCache } from "./state.js";
 
 export interface HierarchyCounts {
   milestones: number;
@@ -25,11 +21,13 @@ export interface HierarchyCounts {
 }
 
 export interface MigrationAutoCheckResult {
-  action: "none" | "imported";
+  action: "none" | "recovery-required";
   reason: "no-markdown" | "in-sync" | "db-empty" | "count-mismatch";
   markdown: HierarchyCounts;
   beforeDb: HierarchyCounts;
   afterDb: HierarchyCounts;
+  recoveryCommand?: string;
+  message?: string;
 }
 
 function zeroCounts(): HierarchyCounts {
@@ -83,7 +81,7 @@ export function countDbHierarchy(): HierarchyCounts {
   return counts;
 }
 
-export async function autoImportMarkdownHierarchyIfDbMismatch(
+export async function checkMarkdownHierarchyAgainstDb(
   basePath: string,
 ): Promise<MigrationAutoCheckResult> {
   const markdown = countMarkdownHierarchy(basePath);
@@ -108,22 +106,16 @@ export async function autoImportMarkdownHierarchyIfDbMismatch(
   }
 
   const reason = sameCounts(beforeDb, zeroCounts()) ? "db-empty" : "count-mismatch";
-  const imported = transaction(() => {
-    clearEngineHierarchy();
-    return migrateHierarchyToDb(basePath);
-  });
-  invalidateStateCache();
-
-  const afterDb = {
-    milestones: imported.milestones,
-    slices: imported.slices,
-    tasks: imported.tasks,
+  return {
+    action: "recovery-required",
+    reason,
+    markdown,
+    beforeDb,
+    afterDb: beforeDb,
+    recoveryCommand: "gsd recover",
+    message:
+      `Markdown planning artifacts (${markdown.milestones}M/${markdown.slices}S/${markdown.tasks}T) ` +
+      `do not match the authoritative DB (${beforeDb.milestones}M/${beforeDb.slices}S/${beforeDb.tasks}T). ` +
+      "Runtime startup will not import markdown automatically; run explicit GSD recovery if markdown should repopulate the database.",
   };
-  if (!sameCounts(markdown, afterDb)) {
-    throw new Error(
-      `migration auto-import verification failed: markdown ${markdown.milestones}M/${markdown.slices}S/${markdown.tasks}T, db ${afterDb.milestones}M/${afterDb.slices}S/${afterDb.tasks}T`,
-    );
-  }
-
-  return { action: "imported", reason, markdown, beforeDb, afterDb };
 }

package/src/resources/extensions/gsd/milestone-actions.ts

@@ -24,6 +24,7 @@ import { deleteMilestone, getMilestone, isDbAvailable, updateMilestoneStatus } f
 import { removeWorktree } from "./worktree-manager.js";
 import { logWarning } from "./workflow-logger.js";
 import { isAutoActive } from "./auto.js";
+import { isClosedStatus } from "./status-guards.js";
 
 /**
  * Writer-side assert for mutations that race with auto-mode's squash merge (#4704).
@@ -44,7 +45,7 @@ function assertNotAutoActive(action: string): void {
 /**
  * Park a milestone — creates a PARKED.md marker file with reason and timestamp.
  * Parked milestones are skipped during active-milestone discovery but stay on disk.
- * Returns true if successfully parked, false if milestone not found or already parked.
+ * Returns true if successfully parked, false if milestone not found, already parked, or complete.
  */
 export function parkMilestone(basePath: string, milestoneId: string, reason: string): boolean {
   assertNotAutoActive("park milestone");
@@ -52,8 +53,13 @@ export function parkMilestone(basePath: string, milestoneId: string, reason: str
   if (!mDir || !existsSync(mDir)) return false;
 
   // Guard: do not park a completed milestone — it would corrupt depends_on satisfaction
-  const summaryFile = resolveMilestoneFile(basePath, milestoneId, "SUMMARY");
-  if (summaryFile) return false;
+  const dbAvailable = isDbAvailable();
+  const milestone = dbAvailable ? getMilestone(milestoneId) : null;
+  if (milestone && isClosedStatus(milestone.status)) return false;
+  if (!dbAvailable) {
+    const summaryFile = resolveMilestoneFile(basePath, milestoneId, "SUMMARY");
+    if (summaryFile) return false;
+  }
 
   const parkedPath = join(mDir, buildMilestoneFileName(milestoneId, "PARKED"));
   if (existsSync(parkedPath)) return false; // already parked
@@ -72,7 +78,7 @@ export function parkMilestone(basePath: string, milestoneId: string, reason: str
 
   writeFileSync(parkedPath, content, "utf-8");
   // Sync DB status so deriveStateFromDb also skips this milestone (#2694)
-  if (isDbAvailable()) {
+  if (dbAvailable) {
     try {
       updateMilestoneStatus(milestoneId, "parked");
     } catch (err) {

package/src/resources/extensions/gsd/native-git-bridge.ts

@@ -6,6 +6,7 @@
 // execSync calls because git2 credential handling is too complex.
 
 import { execSync, execFileSync } from "node:child_process";
+import type { ExecFileSyncOptionsWithStringEncoding } from "node:child_process";
 import { existsSync, readFileSync, unlinkSync, rmSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
 import { GSDError, GSD_GIT_ERROR } from "./errors.js";
@@ -16,6 +17,8 @@ import { isInfrastructureError } from "./auto/infra-errors.js";
 // Issue #453: keep auto-mode bookkeeping on the stable git CLI path unless a
 // caller explicitly opts into the native helper.
 const NATIVE_GSD_GIT_ENABLED = process.env.GSD_ENABLE_NATIVE_GSD_GIT === "1";
+const TRANSIENT_GIT_RETRY_CODES = new Set(["ENOBUFS", "EAGAIN"]);
+const GIT_RETRY_DELAY_MS = 200;
 
 // ─── Native Module Types ──────────────────────────────────────────────────
 
@@ -144,9 +147,46 @@ function gitExec(basePath: string, args: string[], allowFailure = false): string
       encoding: "utf-8",
       env: GIT_NO_PROMPT_ENV,
     }).trim();
-  } catch {
+  } catch (err) {
     if (allowFailure) return "";
-    throw new GSDError(GSD_GIT_ERROR, `git ${args.join(" ")} failed in ${basePath}`);
+    throw new GSDError(GSD_GIT_ERROR, `git ${args.join(" ")} failed in ${basePath}: ${getErrorMessage(err)}`);
+  }
+}
+
+/** sleepSync uses Atomics.wait for a blocking pause without busy-waiting; it blocks the current thread and requires Atomics.wait support. */
+function sleepSync(ms: number): void {
+  Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, ms);
+}
+
+function isRetryableGitError(err: unknown): boolean {
+  const code = isInfrastructureError(err)
+    ?? isInfrastructureError((err as { stderr?: string })?.stderr ?? "");
+  return code !== null && TRANSIENT_GIT_RETRY_CODES.has(code);
+}
+
+function execGitFileSyncWithRetry(
+  basePath: string,
+  args: string[],
+  options: Partial<ExecFileSyncOptionsWithStringEncoding>,
+): string {
+  try {
+    return execFileSync("git", args, {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+      env: GIT_NO_PROMPT_ENV,
+      ...options,
+    }).trim();
+  } catch (err) {
+    if (!isRetryableGitError(err)) throw err;
+    sleepSync(GIT_RETRY_DELAY_MS);
+    return execFileSync("git", args, {
+      cwd: basePath,
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8",
+      env: GIT_NO_PROMPT_ENV,
+      ...options,
+    }).trim();
   }
 }
 
@@ -159,9 +199,9 @@ function gitFileExec(basePath: string, args: string[], allowFailure = false): st
       encoding: "utf-8",
       env: GIT_NO_PROMPT_ENV,
     }).trim();
-  } catch {
+  } catch (err) {
     if (allowFailure) return "";
-    throw new GSDError(GSD_GIT_ERROR, `git ${args.join(" ")} failed in ${basePath}`);
+    throw new GSDError(GSD_GIT_ERROR, `git ${args.join(" ")} failed in ${basePath}: ${getErrorMessage(err)}`);
   }
 }
 
@@ -428,16 +468,21 @@ export function nativeDiffNameStatus(
 
 /**
  * Get numstat diff between two refs.
+ * useMergeBase: if true, uses three-dot semantics.
  * Native: libgit2 patch line stats.
  * Fallback: `git diff --numstat`.
  */
-export function nativeDiffNumstat(basePath: string, fromRef: string, toRef: string): GitNumstat[] {
+export function nativeDiffNumstat(basePath: string, fromRef: string, toRef: string, useMergeBase?: boolean): GitNumstat[] {
   const native = loadNative();
-  if (native) {
+  if (native && !useMergeBase) {
     return native.gitDiffNumstat(basePath, fromRef, toRef);
   }
 
-  const result = gitExec(basePath, ["diff", "--numstat", fromRef, toRef], true);
+  const refspec = useMergeBase ? `${fromRef}...${toRef}` : undefined;
+  const args = refspec
+    ? ["diff", "--numstat", refspec]
+    : ["diff", "--numstat", fromRef, toRef];
+  const result = gitExec(basePath, args, true);
   if (!result) return [];
 
   return result.split("\n").filter(Boolean).map(line => {
@@ -935,13 +980,10 @@ export function nativeCommit(
   try {
     const args = ["commit", "-F", "-"];
     if (options?.allowEmpty) args.push("--allow-empty");
-    const result = execFileSync("git", args, {
-      cwd: basePath,
+    const result = execGitFileSyncWithRetry(basePath, args, {
       stdio: ["pipe", "pipe", "pipe"],
-      encoding: "utf-8",
-      env: GIT_NO_PROMPT_ENV,
       input: message,
-    }).trim();
+    });
     return result;
   } catch (err: unknown) {
     const errObj = err as { stdout?: string; stderr?: string; message?: string };

package/src/resources/extensions/gsd/post-execution-checks.ts

@@ -46,6 +46,46 @@ export interface PostExecutionResult {
 
 // ─── Import Resolution Check ─────────────────────────────────────────────────
 
+/**
+ * Replace the contents of single- and double-quoted string literals on a single
+ * source line with spaces so import patterns do not match text inside strings.
+ * Template-literal spans are handled separately via the inTemplateLiteral flag.
+ */
+function stripStringLiterals(line: string): string {
+  let result = "";
+  let i = 0;
+
+  while (i < line.length) {
+    const ch = line[i];
+
+    if (ch === '"' || ch === "'") {
+      result += ch;
+      i++;
+
+      while (i < line.length) {
+        const c = line[i];
+
+        if (c === "\\" && i + 1 < line.length) {
+          result += "  ";
+          i += 2;
+        } else if (c === ch) {
+          result += ch;
+          i++;
+          break;
+        } else {
+          result += " ";
+          i++;
+        }
+      }
+    } else {
+      result += ch;
+      i++;
+    }
+  }
+
+  return result;
+}
+
 /**
  * Extract relative import paths from TypeScript/JavaScript source code.
  * Returns array of { importPath, lineNum } for relative imports.
@@ -62,14 +102,23 @@ export function extractRelativeImports(
   //   import './path'
   //   require('./path')
   //   require("../path")
-  const importPattern = /(?:import\s+(?:.*?\s+from\s+)?|require\s*\(\s*)(['"])(\.\.?\/[^'"]+)\1/g;
+  const importPattern = /(?:^|[;{}]\s*)import\s+(?:.*?\s+from\s+)?(['"])(\.\.?\/[^'"]+)\1/g;
+  const requirePattern = /require\s*\(\s*(['"])(\.\.?\/[^'"]+)\1/g;
 
   // Track if we're inside a block comment
   let inBlockComment = false;
+  let inTemplateLiteral = false;
 
   for (let i = 0; i < lines.length; i++) {
     const line = lines[i];
 
+    if (inTemplateLiteral) {
+      if ((line.match(/(?<!\\)`/g) ?? []).length % 2 === 1) {
+        inTemplateLiteral = false;
+      }
+      continue;
+    }
+
     // Handle block comment boundaries
     if (inBlockComment) {
       if (line.includes("*/")) {
@@ -101,10 +150,22 @@ export function extractRelativeImports(
 
     // Reset lastIndex for each line
     importPattern.lastIndex = 0;
+    requirePattern.lastIndex = 0;
+
+    const strippedLine = stripStringLiterals(line);
 
     while ((match = importPattern.exec(line)) !== null) {
+      const importOffset = match[0].indexOf("import");
+      const importStart = match.index + importOffset;
+      if (
+        strippedLine.slice(importStart, importStart + "import".length) !==
+        "import"
+      ) {
+        continue;
+      }
+
       // Check if this match is after a // comment marker on the same line
-      const beforeMatch = line.substring(0, match.index);
+      const beforeMatch = strippedLine.substring(0, match.index);
       if (beforeMatch.includes("//")) {
         continue;
       }
@@ -114,6 +175,30 @@ export function extractRelativeImports(
         lineNum: i + 1,
       });
     }
+
+    while ((match = requirePattern.exec(line)) !== null) {
+      if (
+        strippedLine.slice(match.index, match.index + "require".length) !==
+        "require"
+      ) {
+        continue;
+      }
+
+      // Check if this match is after a // comment marker on the same line
+      const beforeMatch = strippedLine.substring(0, match.index);
+      if (beforeMatch.includes("//")) {
+        continue;
+      }
+
+      imports.push({
+        importPath: match[2],
+        lineNum: i + 1,
+      });
+    }
+
+    if ((strippedLine.match(/(?<!\\)`/g) ?? []).length % 2 === 1) {
+      inTemplateLiteral = true;
+    }
   }
 
   return imports;

package/src/resources/extensions/gsd/pre-execution-checks.ts

@@ -23,6 +23,7 @@ import { homedir } from "node:os";
 import { resolve } from "node:path";
 import type { TaskRow } from "./db-task-slice-rows.js";
 import type { PreExecutionCheckJSON } from "./verification-evidence.ts";
+import { validateVerificationCommand } from "./verification-gate.js";
 
 const NPM_COMMAND = process.platform === "win32" ? "npm.cmd" : "npm";
 
@@ -37,6 +38,35 @@ export interface PreExecutionResult {
   durationMs: number;
 }
 
+export function checkVerificationCommands(tasks: TaskRow[]): PreExecutionCheckJSON[] {
+  const results: PreExecutionCheckJSON[] = [];
+
+  for (const task of tasks) {
+    const verify = task.verify.trim();
+    if (!verify) continue;
+
+    const commands = verify
+      .split("&&")
+      .map((command) => command.trim())
+      .filter(Boolean);
+
+    for (const command of commands) {
+      const validation = validateVerificationCommand(command);
+      if (!validation.ok) {
+        results.push({
+          category: "tool",
+          target: `${task.id} Verify`,
+          passed: false,
+          message: `Unsafe or non-runnable Verify command: ${command} (${validation.reason})`,
+          blocking: true,
+        });
+      }
+    }
+  }
+
+  return results;
+}
+
 // ─── Package Existence Check ─────────────────────────────────────────────────
 
 /**
@@ -757,8 +787,9 @@ export async function runPreExecutionChecks(
   const fileChecks = checkFilePathConsistency(tasks, basePath);
   const orderingChecks = checkTaskOrdering(tasks, basePath);
   const contractChecks = checkInterfaceContracts(tasks, basePath);
+  const verificationChecks = checkVerificationCommands(tasks);
 
-  allChecks.push(...fileChecks, ...orderingChecks, ...contractChecks);
+  allChecks.push(...fileChecks, ...orderingChecks, ...contractChecks, ...verificationChecks);
 
   // Run async package checks
   const packageChecks = await checkPackageExistence(tasks, basePath);

package/src/resources/extensions/gsd/prompt-loader.ts

@@ -200,7 +200,7 @@ export function loadPrompt(name: string, vars: Record<string, string> = {}): str
     if (missing.length > 0) {
       throw new GSDError(
         GSD_PARSE_ERROR,
-        `loadPrompt("${name}"): template declares {{${missing.join("}}, {{")}}}} but no value was provided. ` +
+        `loadPrompt("${name}"): template declares {{${missing.join("}}, {{")}}} but no value was provided. ` +
         `This usually means the extension code in memory is older than the template on disk. ` +
         `Restart pi to reload the extension.`,
       );

package/src/resources/extensions/gsd/prompts/complete-milestone.md

@@ -57,7 +57,7 @@ Subagents report only; they do not write user source. Fold any findings into Dec
 **Success path** (all verifications passed):
 
 10. For each requirement whose status changed in step 9, call `gsd_requirement_update` with the requirement ID and updated `status` and `validation` fields — the tool regenerates `.gsd/REQUIREMENTS.md` automatically. Do this BEFORE completing the milestone so requirement updates are persisted.
-11. Update `.gsd/PROJECT.md`: use the `write` tool with `path: ".gsd/PROJECT.md"` and `content` containing the full updated document reflecting milestone completion and current project state. Do NOT use the `edit` tool for this — PROJECT.md is a full-document refresh.
+11. Refresh the project state through `gsd_summary_save` with `artifact_type: "PROJECT"` and the full updated project markdown as `content`; omit `milestone_id`. The tool persists the DB-backed PROJECT artifact and renders `.gsd/PROJECT.md`. Do not write or edit `.gsd/PROJECT.md` directly.
 12. Extract structured learnings from this milestone and persist them to the GSD memory store. Follow the procedure block immediately below — it writes `{{milestoneId}}-LEARNINGS.md` as the audit trail and persists Patterns, Lessons, and Decisions via `capture_thought` (categories: pattern, gotcha/convention, architecture). The memory store is the single source of truth for cross-session durable knowledge (ADR-013).
 
 {{extractLearningsSteps}}

package/src/resources/extensions/gsd/prompts/complete-slice.md

@@ -34,7 +34,7 @@ Use `subagent` only for fresh-context review when useful: reviewer for cross-cut
 12. Review the inlined task-summary excerpts for DECISIONS.md and KNOWLEDGE.md-worthy decisions, patterns, and gotchas. Read full `*-SUMMARY.md` files only when an excerpt is absent, truncated, or lacks the specific evidence needed for the slice narrative. Capture significant items with `capture_thought`; do not append knowledge files directly.
 13. When verification passes, call `gsd_slice_complete`. The DB-backed tool is the canonical write path. Do **not** manually write `{{sliceSummaryPath}}`. Do **not** manually write `{{sliceUatPath}}`. Do not edit roadmap checkboxes; the tool renders files and updates projections.
 14. Do not run git commands.
-15. Update `.gsd/PROJECT.md` with a full `write` only if the current project state needs refresh.
+15. If the current project state needs refresh, call `gsd_summary_save` with `artifact_type: "PROJECT"` and the full updated project markdown as `content`; omit `milestone_id`. Do not write or edit `.gsd/PROJECT.md` directly.
 
 **Autonomous execution:** no human is available. Do not call `ask_user_questions` or `secure_env_collect`; make reasonable assumptions and document them.