gsd-pi 2.82.0 → 3.0.0-dev.04f5ccf82

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 => {
@@ -553,7 +598,10 @@ export function nativeBranchList(basePath: string, pattern?: string): string[] {
   const result = gitFileExec(basePath, args, true);
   if (!result) return [];
 
-  return result.split("\n").map(b => b.trim().replace(/^\* /, "")).filter(Boolean);
+  return result
+    .split("\n")
+    .map(b => b.trim().replace(/^[*+]\s+/, ""))
+    .filter(Boolean);
 }
 
 /**
@@ -935,13 +983,10 @@ 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 };
@@ -949,7 +994,11 @@ export function nativeCommit(
     if (combined.includes("nothing to commit") || combined.includes("nothing added to commit") || combined.includes("no changes added")) {
       return null;
     }
-    throw err;
+    const commitDetail = errObj.stderr?.trim() || errObj.message || "git commit failed";
+    const wrapped = new Error(`git commit failed: ${commitDetail}`);
+    (wrapped as Error & { stdout?: string; stderr?: string }).stdout = errObj.stdout;
+    (wrapped as Error & { stdout?: string; stderr?: string }).stderr = errObj.stderr;
+    throw wrapped;
   }
 }
 

package/src/resources/extensions/gsd/parallel-orchestrator.ts

@@ -1005,6 +1005,9 @@ export function refreshWorkerStatuses(
   for (const [mid, worker] of state.workers) {
     const diskStatus = statusMap.get(mid);
     if (!diskStatus) {
+      if (worker.state === "stopped" || worker.state === "error") {
+        continue;
+      }
       if (!isPidAlive(worker.pid)) {
         worker.cleanup?.();
         worker.cleanup = undefined;

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

@@ -357,6 +357,11 @@ export function resolveGsdPathContract(
   };
 }
 
+export function gsdProjectionRoot(basePath: string): string {
+  const contract = resolveGsdPathContract(basePath);
+  return normalizeRealPath(contract.worktreeGsd ?? contract.projectGsd);
+}
+
 /**
  * Invalidate the gsdRoot cache.
  * Use ONLY at session-reset boundaries: workspace switch, process exit, or

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

@@ -0,0 +1,79 @@
+// GSD-2 — Pending auto-start handoff state.
+// Stores discuss-to-auto handoff entries keyed by project root.
+
+import type { ExtensionAPI, ExtensionCommandContext } from "@gsd/pi-coding-agent";
+import { createWorkspace, scopeMilestone, type MilestoneScope } from "./workspace.js";
+
+export interface PendingAutoStartEntry {
+  ctx: ExtensionCommandContext;
+  pi: ExtensionAPI;
+  basePath: string;
+  milestoneId: string;
+  step?: boolean;
+  createdAt: number;
+  readyRejectCount?: number;
+  scope: MilestoneScope;
+  planBlockedRecoveryCount: number;
+}
+
+export interface PendingAutoStartInput {
+  basePath: string;
+  milestoneId: string;
+  ctx: ExtensionCommandContext;
+  pi: ExtensionAPI;
+  step?: boolean;
+  createdAt?: number;
+}
+
+const pendingAutoStartMap = new Map<string, PendingAutoStartEntry>();
+
+export function getPendingAutoStart(basePath?: string): PendingAutoStartEntry | null {
+  if (basePath) return pendingAutoStartMap.get(basePath) ?? null;
+  if (pendingAutoStartMap.size === 1) return pendingAutoStartMap.values().next().value!;
+  return null;
+}
+
+export const _getPendingAutoStart = getPendingAutoStart;
+
+export function hasPendingAutoStart(basePath?: string): boolean {
+  if (basePath) return pendingAutoStartMap.has(basePath);
+  return pendingAutoStartMap.size > 0;
+}
+
+export function setPendingAutoStart(basePath: string, entry: PendingAutoStartInput): void {
+  if (!entry.ctx || !entry.pi) {
+    throw new Error("setPendingAutoStart requires ctx and pi");
+  }
+  const ws = createWorkspace(entry.basePath);
+  const scope = scopeMilestone(ws, entry.milestoneId);
+  pendingAutoStartMap.set(basePath, {
+    createdAt: Date.now(),
+    planBlockedRecoveryCount: 0,
+    ...entry,
+    scope,
+    ctx: entry.ctx,
+    pi: entry.pi,
+  });
+}
+
+export function deletePendingAutoStart(basePath: string): void {
+  pendingAutoStartMap.delete(basePath);
+}
+
+export function clearPendingAutoStart(basePath?: string): void {
+  if (basePath) {
+    pendingAutoStartMap.delete(basePath);
+  } else {
+    pendingAutoStartMap.clear();
+  }
+}
+
+export function getDiscussionMilestoneId(basePath?: string): string | null {
+  if (basePath) {
+    return pendingAutoStartMap.get(basePath)?.milestoneId ?? null;
+  }
+  if (pendingAutoStartMap.size === 1) {
+    return pendingAutoStartMap.values().next().value!.milestoneId;
+  }
+  return null;
+}

package/src/resources/extensions/gsd/planning-path-scope.ts

@@ -13,6 +13,10 @@ function isInsideBase(basePath: string, candidate: string): boolean {
   return rel === "" || (!!rel && !rel.startsWith("..") && !isAbsolute(rel));
 }
 
+function isInsideAnyBase(bases: string[], candidate: string): boolean {
+  return bases.some((base) => isInsideBase(base, candidate));
+}
+
 /**
  * Planning IO fields are execution contracts. Absolute paths are only safe when
  * they stay inside the active working directory; in worktree mode, an absolute
@@ -21,13 +25,17 @@ function isInsideBase(basePath: string, candidate: string): boolean {
 export function validatePlanningPathScope(
   basePath: string,
   fields: PlanningPathScopeField[],
+  allowedAbsoluteRoots?: string[],
 ): string | null {
+  const absoluteRoots = (allowedAbsoluteRoots && allowedAbsoluteRoots.length > 0)
+    ? allowedAbsoluteRoots
+    : [basePath];
   for (const { field, values } of fields) {
     for (const raw of values) {
       const candidate = normalizePlannedFileReference(raw);
       if (!isAbsolute(candidate)) continue;
-      if (isInsideBase(basePath, candidate)) continue;
-      return `${field} contains absolute path outside working directory: ${candidate}. Use a path relative to ${basePath}.`;
+      if (isInsideAnyBase(absoluteRoots, candidate)) continue;
+      return `${field} contains absolute path outside allowed repository roots: ${candidate}. Use a path relative to one of: ${absoluteRoots.join(", ")}.`;
     }
   }
 

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;
@@ -159,16 +244,6 @@ export function resolveImportPath(
       ".woff", ".woff2", ".ttf", ".otf", ".eot",
     ]);
     const runtimeFallbackExtensions = new Set([".js", ".jsx", ".mjs", ".cjs"]);
-    const dottedStemFallbackExtensions = new Set([".server", ".client", ".webhook"]);
-
-    if (
-      explicitExt !== "" &&
-      !runtimeFallbackExtensions.has(explicitExt) &&
-      !nonFallbackExtensions.has(explicitExt) &&
-      !dottedStemFallbackExtensions.has(explicitExt)
-    ) {
-      return { exists: false, resolvedPath: null };
-    }
 
     if (nonFallbackExtensions.has(explicitExt) && !runtimeFallbackExtensions.has(explicitExt)) {
       return { exists: false, resolvedPath: null };

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

@@ -20,9 +20,10 @@
 import { existsSync } from "node:fs";
 import { spawn } from "node:child_process";
 import { homedir } from "node:os";
-import { resolve } from "node:path";
+import { isAbsolute, relative, 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 +38,39 @@ export interface PreExecutionResult {
   durationMs: number;
 }
 
+export interface PreExecutionCheckContext {
+  additionalRoots?: string[];
+}
+
+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 ─────────────────────────────────────────────────
 
 /**
@@ -105,7 +139,7 @@ export function extractPackageReferences(description: string): string[] {
   while ((importMatch = importPattern.exec(description)) !== null) {
     // Skip relative imports and node builtins
     const pkg = importMatch[1];
-    if (!pkg.startsWith(".") && !pkg.startsWith("node:")) {
+    if (!pkg.startsWith(".") && !pkg.startsWith("node:") && !pkg.startsWith("@/")) {
       packages.add(normalizePackageName(pkg));
     }
   }
@@ -341,7 +375,7 @@ function extractPathFromAnnotation(raw: string): string {
     return quoteMatch[2].trim();
   }
 
-  const annotatedMatch = trimmed.match(/^(.+?)\s+[—–-]\s+.+$/);
+  const annotatedMatch = trimmed.match(/^(.+?)(?:\s+[—–-]\s+.+|\s+\([^()]+\))$/);
   if (annotatedMatch) {
     const prefix = annotatedMatch[1].trim();
     const prefixBacktickMatch = prefix.match(/`([^`]+)`/);
@@ -415,6 +449,14 @@ function containsGlobPattern(candidate: string): boolean {
   return ["*", "?", "[", "]", "{", "}"].some((char) => candidate.includes(char));
 }
 
+function toComparisonPath(filePath: string, basePath: string): string {
+  const normalized = normalizeFilePath(filePath);
+  if (!isAbsolute(normalized)) return normalized;
+  const normalizedBasePath = normalizeFilePath(basePath);
+  const rel = normalizeFilePath(relative(normalizedBasePath, normalized));
+  return rel && !rel.startsWith("..") && rel !== "." ? rel : normalized;
+}
+
 /**
  * Build a set of files that will be created by tasks up to (but not including) taskIndex.
  * Also includes outputs of completed tasks at any position — a completed task has already
@@ -450,9 +492,11 @@ function getExpectedOutputsUpTo(tasks: TaskRow[], taskIndex: number): Set<string
  */
 export function checkFilePathConsistency(
   tasks: TaskRow[],
-  basePath: string
+  basePath: string,
+  context?: PreExecutionCheckContext,
 ): PreExecutionCheckJSON[] {
   const results: PreExecutionCheckJSON[] = [];
+  const resolutionRoots = [basePath, ...(context?.additionalRoots ?? [])];
 
   // Build a set of all files created by any task at any position (normalized).
   // Used to suppress consistency errors for files that will be caught with a
@@ -460,14 +504,16 @@ export function checkFilePathConsistency(
   const allTaskOutputs = new Set<string>();
   for (const t of tasks) {
     for (const f of t.expected_output) {
-      allTaskOutputs.add(normalizeFilePath(f));
+      allTaskOutputs.add(toComparisonPath(f, basePath));
     }
   }
 
   for (let i = 0; i < tasks.length; i++) {
     const task = tasks[i];
-    const priorOutputs = getExpectedOutputsUpTo(tasks, i);
-    const ownOutputs = new Set<string>(task.expected_output.map(normalizeFilePath));
+    const priorOutputs = new Set<string>(
+      Array.from(getExpectedOutputsUpTo(tasks, i), (filePath) => toComparisonPath(filePath, basePath)),
+    );
+    const ownOutputs = new Set<string>(task.expected_output.map((filePath) => toComparisonPath(filePath, basePath)));
     const filesToCheck = [...task.inputs];
 
     for (const file of filesToCheck) {
@@ -476,12 +522,11 @@ export function checkFilePathConsistency(
       if (!shouldValidateInputAsPath(file)) continue;
 
       // Normalize path for consistent comparison
-      const normalizedFile = normalizeFilePath(file);
+      const normalizedFile = toComparisonPath(file, basePath);
       if (containsGlobPattern(normalizedFile)) continue;
 
       // Check if file exists on disk
-      const absolutePath = resolve(basePath, normalizedFile);
-      const existsOnDisk = existsSync(absolutePath);
+      const existsOnDisk = resolutionRoots.some((root) => existsSync(resolve(root, normalizedFile)));
 
       // Check if file is in prior expected outputs (priorOutputs already normalized)
       const inPriorOutputs = priorOutputs.has(normalizedFile);
@@ -527,16 +572,18 @@ export function checkFilePathConsistency(
  */
 export function checkTaskOrdering(
   tasks: TaskRow[],
-  basePath: string
+  basePath: string,
+  context?: PreExecutionCheckContext,
 ): PreExecutionCheckJSON[] {
   const results: PreExecutionCheckJSON[] = [];
+  const resolutionRoots = [basePath, ...(context?.additionalRoots ?? [])];
 
   // Build map: normalized file → task index that creates it
   const fileCreators = new Map<string, { taskId: string; index: number; originalPath: string; completed: boolean }>();
   for (let i = 0; i < tasks.length; i++) {
     const task = tasks[i];
     for (const file of task.expected_output) {
-      const normalizedFile = normalizeFilePath(file);
+      const normalizedFile = toComparisonPath(file, basePath);
       const existing = fileCreators.get(normalizedFile);
       if (!existing || (!existing.completed && task.status === "completed")) {
         fileCreators.set(normalizedFile, {
@@ -560,15 +607,14 @@ export function checkTaskOrdering(
       if (isRuntimeOnlyInput(file)) continue;
       if (!shouldValidateInputAsPath(file)) continue;
 
-      const normalizedFile = normalizeFilePath(file);
+      const normalizedFile = toComparisonPath(file, basePath);
       if (containsGlobPattern(normalizedFile)) continue;
       // A directory reference like `artifacts/M009-S03/` is never a concrete
       // read-before-create dependency: the fileCreators map is keyed by leaf
       // files, and a same-task output under the directory satisfies it.
       if (isDirectoryReference(file)) continue;
       const creator = fileCreators.get(normalizedFile);
-      const absolutePath = resolve(basePath, normalizedFile);
-      const existsOnDisk = existsSync(absolutePath);
+      const existsOnDisk = resolutionRoots.some((root) => existsSync(resolve(root, normalizedFile)));
       // Skip if the creating task has already completed — its output is available
       // regardless of disk state (e.g. file was a temp artifact cleaned up after
       // the task ran, or a replan introduced a new earlier-sequence task that
@@ -748,17 +794,19 @@ export function checkInterfaceContracts(
  */
 export async function runPreExecutionChecks(
   tasks: TaskRow[],
-  basePath: string
+  basePath: string,
+  context?: PreExecutionCheckContext,
 ): Promise<PreExecutionResult> {
   const startTime = Date.now();
   const allChecks: PreExecutionCheckJSON[] = [];
 
   // Run sync checks first
-  const fileChecks = checkFilePathConsistency(tasks, basePath);
-  const orderingChecks = checkTaskOrdering(tasks, basePath);
+  const fileChecks = checkFilePathConsistency(tasks, basePath, context);
+  const orderingChecks = checkTaskOrdering(tasks, basePath, context);
   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/preferences-mcp.ts

@@ -0,0 +1,27 @@
+import type { ClaudeCodeMcpConfig, ClaudeCodeMcpPerModelEntry } from "./preferences-types.js";
+
+/**
+ * Resolve MCP server config for a given model ID using longest-prefix-wins matching.
+ *
+ * Keys in config.per_model are model-ID prefixes. When modelId.startsWith(key),
+ * the key is a candidate; the longest matching key wins. Returns undefined when
+ * no key matches or per_model is empty.
+ */
+export function resolveModelMcpConfig(
+  modelId: string,
+  config: ClaudeCodeMcpConfig,
+): ClaudeCodeMcpPerModelEntry | undefined {
+  let bestKey: string | undefined;
+
+  const perModel = config.per_model ?? {};
+
+  for (const key of Object.keys(perModel)) {
+    if (modelId.startsWith(key)) {
+      if (bestKey === undefined || key.length > bestKey.length) {
+        bestKey = key;
+      }
+    }
+  }
+
+  return bestKey !== undefined ? perModel[bestKey] : undefined;
+}