fix: exclude non-wiped dirs from custom-file scan; warn on non-Claude model profiles (#2511)

* fix(detect-custom-files): exclude skills and command dirs not wiped by installer (closes #2505)

GSD_MANAGED_DIRS included 'skills' and 'command' directories, but the
installer never wipes those paths. Users with third-party skills installed
(40+ files, none in GSD's manifest) had every skill flagged as a "custom
file" requiring backup, producing noisy false-positive reports on every
/gsd-update run.

Removes 'skills' and 'command' from both gsd-tools.cjs and the SDK's
detect-custom-files.ts. Adds two regression tests confirming neither
directory is scanned.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(settings): warn that model profiles are no-ops on non-Claude runtimes (closes #2506)

settings.md presented Quality/Balanced/Budget model profiles without any
indication that these tiers map to Claude models (Opus/Sonnet/Haiku) and
have no effect on non-Claude runtimes (Codex, Gemini CLI, OpenRouter).
Users on Codex saw the profile chooser as if it would meaningfully select
models, but all agents silently used the runtime default regardless.

Adds a non-Claude runtime note before the profile question (shown in
TEXT_MODE, the path all non-Claude runtimes take) explaining the profiles
are no-ops and directing users to either choose Inherit or configure
model_overrides manually. Also updates the Inherit option description to
explicitly name the runtimes where it is the correct choice.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

tests/bug-2506-settings-profile-nonclaude-warning.test.cjs

@@ -0,0 +1,55 @@
+/**
+ * Regression test for bug #2506
+ *
+ * /gsd-settings presents Quality/Balanced/Budget model profiles without any
+ * warning that on non-Claude runtimes (Codex, Gemini CLI, etc.) these profiles
+ * select Claude model tiers and have no effect on actual agent model selection.
+ *
+ * Fix: settings.md must include a non-Claude runtime note instructing users to
+ * use "Inherit" or configure model_overrides manually, and the Inherit option
+ * description must explicitly call out non-Claude runtimes.
+ *
+ * Closes: #2506
+ */
+
+'use strict';
+
+const { describe, test, before } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('fs');
+const path = require('path');
+
+const SETTINGS_PATH = path.join(__dirname, '..', 'get-shit-done', 'workflows', 'settings.md');
+
+describe('bug #2506: settings.md non-Claude runtime warning for model profiles', () => {
+  let content;
+
+  before(() => {
+    content = fs.readFileSync(SETTINGS_PATH, 'utf-8');
+  });
+
+  test('settings.md contains a non-Claude runtime note for model profiles', () => {
+    assert.ok(
+      content.includes('non-Claude runtime') || content.includes('non-Claude runtimes'),
+      'settings.md must include a note about non-Claude runtimes and model profiles'
+    );
+  });
+
+  test('non-Claude note explains profiles are no-ops without model_overrides', () => {
+    assert.ok(
+      content.includes('model_overrides') || content.includes('no effect'),
+      'note must explain profiles have no effect on non-Claude runtimes without model_overrides'
+    );
+  });
+
+  test('Inherit option description explicitly mentions non-Claude runtimes', () => {
+    // The Inherit option in AskUserQuestion must call out non-Claude runtimes
+    const inheritOptionMatch = content.match(/label:\s*"Inherit"[^}]*description:\s*"([^"]+)"/s);
+    assert.ok(inheritOptionMatch, 'Inherit option with label/description must exist in settings.md');
+    const desc = inheritOptionMatch[1];
+    assert.ok(
+      desc.includes('non-Claude') || desc.includes('Codex') || desc.includes('Gemini'),
+      `Inherit option description must mention non-Claude runtimes; got: "${desc}"`
+    );
+  });
+});

tests/update-custom-backup.test.cjs

@@ -225,4 +225,58 @@ describe('detect-custom-files — update workflow backup detection (#1997)', ()
       `should detect custom reference; got: ${JSON.stringify(json.custom_files)}`
     );
   });
+
+  // #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)', () => {
+    writeManifest(tmpDir, {
+      'get-shit-done/workflows/execute-phase.md': '# Execute Phase\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');
+
+    const result = runGsdTools(
+      ['detect-custom-files', '--config-dir', tmpDir],
+      tmpDir
+    );
+
+    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)}`
+    );
+  });
+
+  test('does not scan command/ directory (installer does not wipe it)', () => {
+    writeManifest(tmpDir, {
+      'get-shit-done/workflows/execute-phase.md': '# Execute Phase\n',
+    });
+
+    // Simulate files in command/ dir not wiped by installer
+    const commandDir = path.join(tmpDir, 'command');
+    fs.mkdirSync(commandDir, { recursive: true });
+    fs.writeFileSync(path.join(commandDir, 'user-command.md'), '# User Command\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);
+    const commandFiles = json.custom_files.filter(f => f.startsWith('command/'));
+    assert.strictEqual(
+      commandFiles.length, 0,
+      `command/ should not be scanned; got false positives: ${JSON.stringify(commandFiles)}`
+    );
+  });
 });