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/query/registry.ts

@@ -0,0 +1,121 @@
+/**
+ * Query command registry — routes commands to native SDK handlers.
+ *
+ * The registry is a flat `Map<string, QueryHandler>` that maps command names
+ * to handler functions. Unknown commands throw GSDError — the gsd-tools.cjs
+ * fallback was removed in v3.0 when all commands were migrated to native handlers.
+ *
+ * Also exports `extractField` — a TypeScript port of the `--pick` field
+ * extraction logic from gsd-tools.cjs (lines 365-382).
+ *
+ * @example
+ * ```typescript
+ * import { QueryRegistry, extractField } from './registry.js';
+ *
+ * const registry = new QueryRegistry();
+ * registry.register('generate-slug', generateSlug);
+ * const result = await registry.dispatch('generate-slug', ['My Phase'], '/project');
+ * const slug = extractField(result.data, 'slug'); // 'my-phase'
+ * ```
+ */
+
+import type { QueryResult, QueryHandler } from './utils.js';
+import { GSDError, ErrorClassification } from '../errors.js';
+
+// ─── extractField ──────────────────────────────────────────────────────────
+
+/**
+ * Extract a nested field from an object using dot-notation and bracket syntax.
+ *
+ * Direct port of `extractField()` from gsd-tools.cjs (lines 365-382).
+ * Supports `a.b.c` dot paths, `items[0]` array indexing, and `items[-1]`
+ * negative indexing.
+ *
+ * @param obj - The object to extract from
+ * @param fieldPath - Dot-separated path with optional bracket notation
+ * @returns The extracted value, or undefined if the path doesn't resolve
+ */
+export function extractField(obj: unknown, fieldPath: string): unknown {
+  const parts = fieldPath.split('.');
+  let current: unknown = obj;
+  for (const part of parts) {
+    if (current === null || current === undefined) return undefined;
+    const bracketMatch = part.match(/^(.+?)\[(-?\d+)]$/);
+    if (bracketMatch) {
+      const key = bracketMatch[1];
+      const index = parseInt(bracketMatch[2], 10);
+      current = (current as Record<string, unknown>)[key];
+      if (!Array.isArray(current)) return undefined;
+      current = index < 0 ? current[current.length + index] : current[index];
+    } else {
+      current = (current as Record<string, unknown>)[part];
+    }
+  }
+  return current;
+}
+
+// ─── QueryRegistry ─────────────────────────────────────────────────────────
+
+/**
+ * Flat command registry that routes query commands to native handlers.
+ *
+ * Unknown commands throw `GSDError` from `dispatch()` — there is no fallback
+ * to gsd-tools.cjs (bridge removed in v3.0). All supported commands must be
+ * registered via `register()`.
+ */
+export class QueryRegistry {
+  private handlers = new Map<string, QueryHandler>();
+
+  /**
+   * Register a native handler for a command name.
+   *
+   * @param command - The command name (e.g., 'generate-slug', 'state.load')
+   * @param handler - The handler function to invoke
+   */
+  register(command: string, handler: QueryHandler): void {
+    this.handlers.set(command, handler);
+  }
+
+  /**
+   * Check if a command has a registered native handler.
+   *
+   * @param command - The command name to check
+   * @returns True if the command has a native handler
+   */
+  has(command: string): boolean {
+    return this.handlers.has(command);
+  }
+
+  /**
+   * Get the handler for a command without dispatching.
+   *
+   * @param command - The command name to look up
+   * @returns The handler function, or undefined if not registered
+   */
+  getHandler(command: string): QueryHandler | undefined {
+    return this.handlers.get(command);
+  }
+
+  /**
+   * Dispatch a command to its registered native handler.
+   *
+   * Throws GSDError for unknown commands — the gsd-tools.cjs fallback was
+   * removed in v3.0. All commands must be registered as native handlers (T-14-13).
+   *
+   * @param command - The command name to dispatch
+   * @param args - Arguments to pass to the handler
+   * @param projectDir - The project directory for context
+   * @returns The query result from the handler
+   * @throws GSDError if no handler is registered for the command
+   */
+  async dispatch(command: string, args: string[], projectDir: string): Promise<QueryResult> {
+    const handler = this.handlers.get(command);
+    if (!handler) {
+      throw new GSDError(
+        `Unknown command: "${command}". No native handler registered.`,
+        ErrorClassification.Validation,
+      );
+    }
+    return handler(args, projectDir);
+  }
+}