diff --git a/get-shit-done/bin/gsd-tools.cjs b/get-shit-done/bin/gsd-tools.cjs
index ca73430d2..de5f3e791 100755
--- a/get-shit-done/bin/gsd-tools.cjs
+++ b/get-shit-done/bin/gsd-tools.cjs
@@ -1070,6 +1070,7 @@ async function runCommand(command, args, cwd, raw, defaultValue) {
         'agents',
         path.join('commands', 'gsd'),
         'hooks',
+        'skills',
       ];
 
       function walkDir(dir, baseDir) {
diff --git a/tests/bug-2942-detect-custom-skills.test.cjs b/tests/bug-2942-detect-custom-skills.test.cjs
new file mode 100644
index 000000000..20e9992b5
--- /dev/null
+++ b/tests/bug-2942-detect-custom-skills.test.cjs
@@ -0,0 +1,177 @@
+/**
+ * GSD Tools Tests — detect-custom-files misses skills/ directory (#2942)
+ *
+ * After v1.39.0 skill consolidation (#2790), skills/ became a GSD-managed root.
+ * GSD_MANAGED_DIRS was missing 'skills', so user-added skill directories like
+ * skills/custom-skill/SKILL.md were never walked and got silently destroyed
+ * during /gsd-update.
+ */
+
+'use strict';
+
+const { describe, test, beforeEach, afterEach } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('fs');
+const path = require('path');
+const crypto = require('crypto');
+const { runGsdTools, createTempDir, cleanup } = require('./helpers.cjs');
+
+function sha256(content) {
+  return crypto.createHash('sha256').update(content).digest('hex');
+}
+
+/**
+ * Write a fake gsd-file-manifest.json into configDir with the given file entries.
+ * Each entry is also written to disk so the directory structure exists.
+ */
+function writeManifest(configDir, files) {
+  const manifest = {
+    version: '1.39.0',
+    timestamp: new Date().toISOString(),
+    files: {}
+  };
+  for (const [relPath, content] of Object.entries(files)) {
+    const fullPath = path.join(configDir, relPath);
+    fs.mkdirSync(path.dirname(fullPath), { recursive: true });
+    fs.writeFileSync(fullPath, content);
+    manifest.files[relPath] = sha256(content);
+  }
+  fs.writeFileSync(
+    path.join(configDir, 'gsd-file-manifest.json'),
+    JSON.stringify(manifest, null, 2)
+  );
+}
+
+/**
+ * Write a file inside configDir (creating parent dirs), but do NOT add it to the manifest.
+ */
+function writeCustomFile(configDir, relPath, content) {
+  const fullPath = path.join(configDir, relPath);
+  fs.mkdirSync(path.dirname(fullPath), { recursive: true });
+  fs.writeFileSync(fullPath, content);
+}
+
+describe('detect-custom-files — skills/ directory missing from GSD_MANAGED_DIRS (#2942)', () => {
+  let tmpDir;
+
+  beforeEach(() => {
+    tmpDir = createTempDir('gsd-2942-skills-');
+  });
+
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  // Test 1: detects custom skill in skills/<name>/SKILL.md
+  test('detects custom skill file at skills/<name>/SKILL.md', () => {
+    writeManifest(tmpDir, {
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+
+    // User-added custom skill — NOT in manifest
+    writeCustomFile(tmpDir, 'skills/test-custom/SKILL.md', '# My Custom Skill\n');
+
+    const result = runGsdTools(
+      ['detect-custom-files', '--config-dir', tmpDir],
+      tmpDir
+    );
+
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const json = JSON.parse(result.output);
+    assert.ok(Array.isArray(json.custom_files), 'custom_files should be an array');
+    assert.ok(json.custom_count >= 1, `custom_count should be >= 1, got ${json.custom_count}`);
+    assert.ok(
+      json.custom_files.includes('skills/test-custom/SKILL.md'),
+      `skills/test-custom/SKILL.md should be in custom_files; got: ${JSON.stringify(json.custom_files)}`
+    );
+  });
+
+  // Test 2: does not flag GSD-owned skills as custom (manifest-tracked path NOT in custom_files)
+  test('does not flag GSD-owned skill as custom when it is tracked in manifest', () => {
+    writeManifest(tmpDir, {
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+
+    // No extra files — only the manifest-tracked skill exists
+
+    const result = runGsdTools(
+      ['detect-custom-files', '--config-dir', tmpDir],
+      tmpDir
+    );
+
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const json = JSON.parse(result.output);
+    assert.ok(Array.isArray(json.custom_files), 'custom_files should be an array');
+    assert.ok(
+      !json.custom_files.includes('skills/gsd-planner/SKILL.md'),
+      `GSD-owned skill should NOT be in custom_files; got: ${JSON.stringify(json.custom_files)}`
+    );
+  });
+
+  // Test 3: regression guard — still detects custom files in get-shit-done/workflows/
+  test('regression: still detects custom files in get-shit-done/workflows/', () => {
+    writeManifest(tmpDir, {
+      'get-shit-done/workflows/plan-phase.md': '# Plan Phase\n',
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+
+    writeCustomFile(tmpDir, 'get-shit-done/workflows/custom-workflow.md', '# My Custom Workflow\n');
+
+    const result = runGsdTools(
+      ['detect-custom-files', '--config-dir', tmpDir],
+      tmpDir
+    );
+
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const json = JSON.parse(result.output);
+    assert.ok(
+      json.custom_files.includes('get-shit-done/workflows/custom-workflow.md'),
+      `custom workflow should still be detected; got: ${JSON.stringify(json.custom_files)}`
+    );
+  });
+
+  // Test 4: custom_count matches custom_files.length
+  test('custom_count matches custom_files.length when multiple custom skills exist', () => {
+    writeManifest(tmpDir, {
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+
+    writeCustomFile(tmpDir, 'skills/test-custom/SKILL.md', '# Custom Skill One\n');
+    writeCustomFile(tmpDir, 'skills/another-custom/SKILL.md', '# Custom Skill Two\n');
+
+    const result = runGsdTools(
+      ['detect-custom-files', '--config-dir', tmpDir],
+      tmpDir
+    );
+
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const json = JSON.parse(result.output);
+    assert.strictEqual(
+      json.custom_count,
+      json.custom_files.length,
+      `custom_count (${json.custom_count}) should equal custom_files.length (${json.custom_files.length})`
+    );
+    assert.strictEqual(json.custom_count, 2, 'should detect exactly 2 custom skill files');
+  });
+
+  // Test 5: manifest_found: true when manifest is present
+  test('manifest_found is true when manifest is present', () => {
+    writeManifest(tmpDir, {
+      'skills/gsd-planner/SKILL.md': '# GSD Planner Skill\n',
+    });
+
+    const result = runGsdTools(
+      ['detect-custom-files', '--config-dir', tmpDir],
+      tmpDir
+    );
+
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const json = JSON.parse(result.output);
+    assert.strictEqual(json.manifest_found, true, 'manifest_found should be true');
+  });
+});
diff --git a/tests/update-custom-backup.test.cjs b/tests/update-custom-backup.test.cjs
index 1bdfcc662..c07679a74 100644
--- a/tests/update-custom-backup.test.cjs
+++ b/tests/update-custom-backup.test.cjs
@@ -226,19 +226,20 @@ describe('detect-custom-files — update workflow backup detection (#1997)', ()
     );
   });
 
-  // #2505 — installer does NOT wipe skills/ or command/; scanning them produces
-  // false-positive "custom file" reports for every skill the user has installed
-  // from other packages.
-  test('does not scan skills/ directory (installer does not wipe it)', () => {
+  // After v1.39.0 skill consolidation (#2790), the installer wipes skills/ on
+  // update. skills/ is now a GSD-managed directory and must be scanned so that
+  // user-added skill directories are backed up before the wipe (#2942).
+  // GSD-owned skills (tracked in manifest) must NOT be flagged as custom.
+  test('scans skills/ directory and detects user-added skills not in manifest (#2942)', () => {
     writeManifest(tmpDir, {
       'get-shit-done/workflows/execute-phase.md': '# Execute Phase\n',
+      'skills/gsd-planner/SKILL.md': '# GSD Planner\n',
     });
 
-    // Simulate user having third-party skills installed — none in manifest
-    const skillsDir = path.join(tmpDir, 'skills');
-    fs.mkdirSync(skillsDir, { recursive: true });
-    fs.writeFileSync(path.join(skillsDir, 'my-custom-skill.md'), '# My Skill\n');
-    fs.writeFileSync(path.join(skillsDir, 'another-plugin-skill.md'), '# Another\n');
+    // Simulate user having a custom skill installed — NOT in manifest
+    const customSkillDir = path.join(tmpDir, 'skills', 'my-custom-skill');
+    fs.mkdirSync(customSkillDir, { recursive: true });
+    fs.writeFileSync(path.join(customSkillDir, 'SKILL.md'), '# My Custom Skill\n');
 
     const result = runGsdTools(
       ['detect-custom-files', '--config-dir', tmpDir],
@@ -248,10 +249,17 @@ describe('detect-custom-files — update workflow backup detection (#1997)', ()
     assert.ok(result.success, `Command failed: ${result.error}`);
 
     const json = JSON.parse(result.output);
-    const skillFiles = json.custom_files.filter(f => f.startsWith('skills/'));
-    assert.strictEqual(
-      skillFiles.length, 0,
-      `skills/ should not be scanned; got false positives: ${JSON.stringify(skillFiles)}`
+
+    // The user's custom skill should be detected
+    assert.ok(
+      json.custom_files.includes('skills/my-custom-skill/SKILL.md'),
+      `custom skill should be detected; got: ${JSON.stringify(json.custom_files)}`
+    );
+
+    // The GSD-owned skill (in manifest) should NOT be flagged as custom
+    assert.ok(
+      !json.custom_files.includes('skills/gsd-planner/SKILL.md'),
+      `GSD-owned skill should not be flagged as custom; got: ${JSON.stringify(json.custom_files)}`
     );
   });