diff --git a/get-shit-done/bin/gsd-tools.cjs b/get-shit-done/bin/gsd-tools.cjs
index 9b07624d9..7d8a398a6 100755
--- a/get-shit-done/bin/gsd-tools.cjs
+++ b/get-shit-done/bin/gsd-tools.cjs
@@ -1204,10 +1204,6 @@ async function runCommand(command, args, cwd, raw, defaultValue) {
         'agents',
         path.join('commands', 'gsd'),
         'hooks',
-        // OpenCode/Kilo flat command dir
-        'command',
-        // Codex/Copilot skills dir
-        'skills',
       ];
 
       function walkDir(dir, baseDir) {
diff --git a/get-shit-done/workflows/settings.md b/get-shit-done/workflows/settings.md
index c87ce8f8d..5c86eedb8 100644
--- a/get-shit-done/workflows/settings.md
+++ b/get-shit-done/workflows/settings.md
@@ -51,6 +51,17 @@ Parse current values (default to `true` if not present):
 <step name="present_settings">
 
 **Text mode (`workflow.text_mode: true` in config or `--text` flag):** Set `TEXT_MODE=true` if `--text` is present in `$ARGUMENTS` OR `text_mode` from init JSON is `true`. When TEXT_MODE is active, replace every `AskUserQuestion` call with a plain-text numbered list and ask the user to type their choice number. This is required for non-Claude runtimes (OpenAI Codex, Gemini CLI, etc.) where `AskUserQuestion` is not available.
+
+**Non-Claude runtime note:** If `TEXT_MODE` is active (i.e. the runtime is non-Claude), prepend the following notice before the model profile question:
+
+```
+Note: Quality, Balanced, and Budget profiles select Claude model tiers (Opus/Sonnet/Haiku).
+On non-Claude runtimes (Codex, Gemini CLI, etc.) these profiles have no effect on actual
+model selection — GSD agents will use the runtime's default model.
+Choose "Inherit" to use the session model for all agents, or configure model_overrides
+manually in .planning/config.json to target specific models for this runtime.
+```
+
 Use AskUserQuestion with current values pre-selected:
 
 ```
@@ -60,10 +71,10 @@ AskUserQuestion([
     header: "Model",
     multiSelect: false,
     options: [
-      { label: "Quality", description: "Opus everywhere except verification (highest cost)" },
-      { label: "Balanced (Recommended)", description: "Opus for planning, Sonnet for research/execution/verification" },
-      { label: "Budget", description: "Sonnet for writing, Haiku for research/verification (lowest cost)" },
-      { label: "Inherit", description: "Use current session model for all agents (best for OpenRouter, local models, or runtime model switching)" }
+      { label: "Quality", description: "Opus everywhere except verification (highest cost) — Claude only" },
+      { label: "Balanced (Recommended)", description: "Opus for planning, Sonnet for research/execution/verification — Claude only" },
+      { label: "Budget", description: "Sonnet for writing, Haiku for research/verification (lowest cost) — Claude only" },
+      { label: "Inherit", description: "Use current session model for all agents (required for non-Claude runtimes: Codex, Gemini CLI, OpenRouter, local models)" }
     ]
   },
   {
diff --git a/sdk/src/query/detect-custom-files.ts b/sdk/src/query/detect-custom-files.ts
index e0975e0a0..2f496bebe 100644
--- a/sdk/src/query/detect-custom-files.ts
+++ b/sdk/src/query/detect-custom-files.ts
@@ -14,8 +14,6 @@ const GSD_MANAGED_DIRS = [
   'agents',
   join('commands', 'gsd'),
   'hooks',
-  'command',
-  'skills',
 ];
 
 function walkDir(dir: string, baseDir: string): string[] {
diff --git a/tests/bug-2506-settings-profile-nonclaude-warning.test.cjs b/tests/bug-2506-settings-profile-nonclaude-warning.test.cjs
new file mode 100644
index 000000000..870395c36
--- /dev/null
+++ b/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}"`
+    );
+  });
+});
diff --git a/tests/update-custom-backup.test.cjs b/tests/update-custom-backup.test.cjs
index 065ef6627..1bdfcc662 100644
--- a/tests/update-custom-backup.test.cjs
+++ b/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)}`
+    );
+  });
 });