diff --git a/.changeset/wise-rams-gather.md b/.changeset/wise-rams-gather.md
new file mode 100644
index 000000000..329aac1c3
--- /dev/null
+++ b/.changeset/wise-rams-gather.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 3318
+---
+**`detect-custom-files` now scans `skills/`** — SDK port omitted `skills` from `GSD_MANAGED_DIRS`, so user-added skills under `<config-dir>/skills/<name>/` were never detected and got silently destroyed during `/gsd-update` (no entry written to `gsd-user-files-backup/`). One-line parity with `bin/gsd-tools.cjs`. (#3317)
diff --git a/sdk/src/query/detect-custom-files.test.ts b/sdk/src/query/detect-custom-files.test.ts
new file mode 100644
index 000000000..2b78b4851
--- /dev/null
+++ b/sdk/src/query/detect-custom-files.test.ts
@@ -0,0 +1,115 @@
+/**
+ * Regression test for #3317 — SDK detect-custom-files omits `skills/` from
+ * GSD_MANAGED_DIRS. Mirrors the CJS-side coverage in
+ * `tests/bug-2942-detect-custom-skills.test.cjs`.
+ *
+ * Without the fix, user-added skills under `<config-dir>/skills/<name>/`
+ * are not detected and get silently wiped on `/gsd-update`.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtemp, mkdir, rm, writeFile } from 'node:fs/promises';
+import { createHash } from 'node:crypto';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+
+import { detectCustomFiles } from './detect-custom-files.js';
+
+function sha256(content: string): string {
+  return createHash('sha256').update(content).digest('hex');
+}
+
+async function writeManifest(configDir: string, files: Record<string, string>): Promise<void> {
+  const manifest = {
+    version: '1.41.1',
+    timestamp: new Date().toISOString(),
+    files: {} as Record<string, string>,
+  };
+  for (const [relPath, content] of Object.entries(files)) {
+    const fullPath = join(configDir, relPath);
+    await mkdir(join(fullPath, '..'), { recursive: true });
+    await writeFile(fullPath, content);
+    manifest.files[relPath] = sha256(content);
+  }
+  await writeFile(
+    join(configDir, 'gsd-file-manifest.json'),
+    JSON.stringify(manifest, null, 2),
+  );
+}
+
+async function writeCustomFile(configDir: string, relPath: string, content: string): Promise<void> {
+  const fullPath = join(configDir, relPath);
+  await mkdir(join(fullPath, '..'), { recursive: true });
+  await writeFile(fullPath, content);
+}
+
+interface DetectResult {
+  custom_files: string[];
+  custom_count: number;
+  manifest_found: boolean;
+}
+
+describe('detectCustomFiles — skills/ parity with CJS port (#3317)', () => {
+  let tmpDir: string;
+
+  beforeEach(async () => {
+    tmpDir = await mkdtemp(join(tmpdir(), 'gsd-3317-skills-'));
+  });
+
+  afterEach(async () => {
+    await rm(tmpDir, { recursive: true, force: true });
+  });
+
+  it('detects custom skill at skills/<name>/SKILL.md', async () => {
+    await writeManifest(tmpDir, {
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+    await writeCustomFile(tmpDir, 'skills/test-custom/SKILL.md', '# My Custom Skill\n');
+
+    const { data } = await detectCustomFiles(['--config-dir', tmpDir], tmpDir);
+    const result = data as DetectResult;
+
+    expect(Array.isArray(result.custom_files)).toBe(true);
+    expect(result.custom_files).toContain('skills/test-custom/SKILL.md');
+    expect(result.custom_count).toBeGreaterThanOrEqual(1);
+  });
+
+  it('does not flag GSD-owned skill listed in manifest', async () => {
+    await writeManifest(tmpDir, {
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+
+    const { data } = await detectCustomFiles(['--config-dir', tmpDir], tmpDir);
+    const result = data as DetectResult;
+
+    expect(result.custom_files).not.toContain('skills/gsd-planner/SKILL.md');
+  });
+
+  it('still detects custom files in get-shit-done/workflows/ (regression guard)', async () => {
+    await writeManifest(tmpDir, {
+      'get-shit-done/workflows/plan-phase.md': '# Plan Phase\n',
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+    await writeCustomFile(tmpDir, 'get-shit-done/workflows/custom-workflow.md', '# Custom\n');
+
+    const { data } = await detectCustomFiles(['--config-dir', tmpDir], tmpDir);
+    const result = data as DetectResult;
+
+    expect(result.custom_files).toContain('get-shit-done/workflows/custom-workflow.md');
+  });
+
+  it('custom_count matches custom_files.length across multiple skills', async () => {
+    await writeManifest(tmpDir, {
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+    await writeCustomFile(tmpDir, 'skills/test-custom/SKILL.md', '# Custom One\n');
+    await writeCustomFile(tmpDir, 'skills/another-custom/SKILL.md', '# Custom Two\n');
+
+    const { data } = await detectCustomFiles(['--config-dir', tmpDir], tmpDir);
+    const result = data as DetectResult;
+
+    expect(result.custom_count).toBe(result.custom_files.length);
+    const skillEntries = result.custom_files.filter(f => f.startsWith('skills/'));
+    expect(skillEntries).toHaveLength(2);
+  });
+});
diff --git a/sdk/src/query/detect-custom-files.ts b/sdk/src/query/detect-custom-files.ts
index 2f496bebe..3dc46fea2 100644
--- a/sdk/src/query/detect-custom-files.ts
+++ b/sdk/src/query/detect-custom-files.ts
@@ -14,6 +14,7 @@ const GSD_MANAGED_DIRS = [
   'agents',
   join('commands', 'gsd'),
   'hooks',
+  'skills',
 ];
 
 function walkDir(dir: string, baseDir: string): string[] {