fix(2137): skip worktree isolation when .gitmodules detected (#2144)

* feat(sdk): add typed query foundation and gsd-sdk query (Phase 1)

Add sdk/src/query registry and handlers with tests, GSDQueryError, CLI query wiring, and supporting type/tool-scoping hooks. Update CHANGELOG. Vitest 4 constructor mock fixes in milestone-runner tests.

Made-with: Cursor

* fix(2137): skip worktree isolation when .gitmodules detected

When a project contains git submodules, worktree isolation cannot
correctly handle submodule commits — three separate gaps exist in
worktree setup, executor commit protocol, and merge-back. Rather
than patch each gap individually, detect .gitmodules at phase start
and fall back to sequential execution, which handles submodules
transparently (Option B).

Affected workflows: execute-phase.md, quick.md

---------

Co-authored-by: David Sienkowski <dave@sienkowski.com>

sdk/src/errors.ts

@@ -0,0 +1,72 @@
+/**
+ * Error classification system for the GSD SDK.
+ *
+ * Provides a taxonomy of error types with semantic exit codes,
+ * enabling CLI consumers and agents to distinguish between
+ * validation failures, execution errors, blocked states, and
+ * interruptions.
+ *
+ * @example
+ * ```typescript
+ * import { GSDError, ErrorClassification, exitCodeFor } from './errors.js';
+ *
+ * throw new GSDError('missing required arg', ErrorClassification.Validation);
+ * // CLI catch handler: process.exitCode = exitCodeFor(err.classification); // 10
+ * ```
+ */
+
+// ─── Error Classification ───────────────────────────────────────────────────
+
+/** Classifies SDK errors into semantic categories for exit code mapping. */
+export enum ErrorClassification {
+  /** Bad input, missing args, schema violations. Exit code 10. */
+  Validation = 'validation',
+
+  /** Runtime failure, file I/O, parse errors. Exit code 1. */
+  Execution = 'execution',
+
+  /** Dependency missing, phase not found. Exit code 11. */
+  Blocked = 'blocked',
+
+  /** Timeout, signal, user cancel. Exit code 1. */
+  Interruption = 'interruption',
+}
+
+// ─── GSDError ───────────────────────────────────────────────────────────────
+
+/**
+ * Base error class for the GSD SDK with classification support.
+ *
+ * @param message - Human-readable error description
+ * @param classification - Error category for exit code mapping
+ */
+export class GSDError extends Error {
+  readonly name = 'GSDError';
+  readonly classification: ErrorClassification;
+
+  constructor(message: string, classification: ErrorClassification) {
+    super(message);
+    this.classification = classification;
+  }
+}
+
+// ─── Exit code mapping ──────────────────────────────────────────────────────
+
+/**
+ * Maps an error classification to a semantic exit code.
+ *
+ * @param classification - The error classification to map
+ * @returns Numeric exit code: 10 (validation), 11 (blocked), 1 (execution/interruption)
+ */
+export function exitCodeFor(classification: ErrorClassification): number {
+  switch (classification) {
+    case ErrorClassification.Validation:
+      return 10;
+    case ErrorClassification.Blocked:
+      return 11;
+    case ErrorClassification.Execution:
+    case ErrorClassification.Interruption:
+    default:
+      return 1;
+  }
+}