diff --git a/.changeset/witty-hawks-jump.md b/.changeset/witty-hawks-jump.md
new file mode 100644
index 000000000..c5a3cadaa
--- /dev/null
+++ b/.changeset/witty-hawks-jump.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 2973
+---
+/gsd-profile-user --refresh writes dev-preferences.md to ~/.claude/skills/gsd-dev-preferences/SKILL.md instead of the legacy commands/gsd/ directory. Installer migrates any preserved legacy file to the new location. See #2973.
diff --git a/bin/install.js b/bin/install.js
index 0426fd583..390f912d5 100755
--- a/bin/install.js
+++ b/bin/install.js
@@ -5325,6 +5325,30 @@ function copyCommandsAsClaudeSkills(srcDir, skillsDir, prefix, pathPrefix, runti
 
   fs.mkdirSync(skillsDir, { recursive: true });
 
+  // #2973 (CR follow-up on #3003): preserve user-generated skills across the
+  // wipe-and-replace. `gsd-dev-preferences/SKILL.md` is written by the user
+  // via `/gsd-profile-user --refresh`; it is NOT shipped by the npm package,
+  // so a wipe without snapshot deletes the user's content with nothing to
+  // restore from. Snapshot the SKILL.md (and any sibling files in that
+  // directory) before the wipe and restore them after.
+  const USER_OWNED_SKILLS = new Set(['gsd-dev-preferences']);
+  const preservedUserSkills = new Map(); // skillName -> Map(relPath -> Buffer)
+  for (const skillName of USER_OWNED_SKILLS) {
+    const skillDir = path.join(skillsDir, skillName);
+    if (!fs.existsSync(skillDir)) continue;
+    const files = new Map();
+    const walkSnap = (curRel, curAbs) => {
+      for (const e of fs.readdirSync(curAbs, { withFileTypes: true })) {
+        const childRel = curRel ? path.join(curRel, e.name) : e.name;
+        const childAbs = path.join(curAbs, e.name);
+        if (e.isDirectory()) walkSnap(childRel, childAbs);
+        else if (e.isFile()) files.set(childRel, fs.readFileSync(childAbs));
+      }
+    };
+    walkSnap('', skillDir);
+    if (files.size > 0) preservedUserSkills.set(skillName, files);
+  }
+
   // Remove previous GSD Claude skills to avoid stale command skills
   const existing = fs.readdirSync(skillsDir, { withFileTypes: true });
   for (const entry of existing) {
@@ -5333,6 +5357,22 @@ function copyCommandsAsClaudeSkills(srcDir, skillsDir, prefix, pathPrefix, runti
     }
   }
 
+  // Restore user-owned skills after the wipe but before recursive copy populates
+  // shipped skills. If the npm package later happens to ship a same-named skill
+  // (currently it does not for gsd-dev-preferences), the restored user content
+  // is the source of truth: the recurse() loop below would overwrite it on
+  // collision, but the USER_OWNED_SKILLS set is by definition disjoint from
+  // shipped-skill names.
+  for (const [skillName, files] of preservedUserSkills) {
+    const skillDir = path.join(skillsDir, skillName);
+    fs.mkdirSync(skillDir, { recursive: true });
+    for (const [relPath, buf] of files) {
+      const absPath = path.join(skillDir, relPath);
+      fs.mkdirSync(path.dirname(absPath), { recursive: true });
+      fs.writeFileSync(absPath, buf);
+    }
+  }
+
   function recurse(currentSrcDir, currentPrefix) {
     const entries = fs.readdirSync(currentSrcDir, { withFileTypes: true });
 
@@ -5519,6 +5559,33 @@ function restoreUserArtifacts(destDir, saved) {
   }
 }
 
+/**
+ * Migrate a legacy dev-preferences.md (saved from commands/gsd/) into the
+ * skills/gsd-dev-preferences/SKILL.md location used by the writer after #2973.
+ *
+ * Skips silently if no legacy file was preserved, or if a SKILL.md already
+ * exists at the new location (don't clobber user-customized skill content
+ * — they may have edited the new file directly). Returns true on actual
+ * migration so callers can log a one-line confirmation.
+ *
+ * @param {string} targetDir - Resolved runtime config directory (e.g. ~/.claude)
+ * @param {Map<string, string>} saved - Map returned by preserveUserArtifacts
+ * @returns {boolean} - true if a file was migrated, false otherwise
+ */
+function migrateLegacyDevPreferencesToSkill(targetDir, saved) {
+  if (!saved || !saved.has('dev-preferences.md')) return false;
+  const skillDir = path.join(targetDir, 'skills', 'gsd-dev-preferences');
+  const skillFile = path.join(skillDir, 'SKILL.md');
+  if (fs.existsSync(skillFile)) return false;
+  try {
+    fs.mkdirSync(skillDir, { recursive: true });
+    fs.writeFileSync(skillFile, saved.get('dev-preferences.md'), 'utf8');
+    return true;
+  } catch {
+    return false;
+  }
+}
+
 /**
  * Recursively copy directory, replacing paths in .md files
  * Deletes existing destDir first to remove orphaned files from previous versions
@@ -6038,7 +6105,14 @@ function uninstall(isGlobal, runtime = 'claude') {
       fs.rmSync(legacyCommandsDir, { recursive: true });
       removedCount++;
       console.log(`  ${green}✓${reset} Removed legacy commands/gsd/`);
+      // #2973: also migrate dev-preferences.md content into the new
+      // skills/gsd-dev-preferences/SKILL.md location (skills-aware runtimes).
+      // This prevents the legacy file from being orphaned after the writer
+      // starts targeting the skills path. No-op if SKILL.md already exists.
       restoreUserArtifacts(legacyCommandsDir, savedLegacyArtifacts);
+      if (migrateLegacyDevPreferencesToSkill(targetDir, savedLegacyArtifacts)) {
+        console.log(`  ${green}✓${reset} Migrated dev-preferences.md → skills/gsd-dev-preferences/SKILL.md (#2973)`);
+      }
     }
   } else if (isHermes) {
     // Hermes Agent: skills live under skills/gsd/ as a single category (per
@@ -6076,7 +6150,14 @@ function uninstall(isGlobal, runtime = 'claude') {
       fs.rmSync(legacyCommandsDir, { recursive: true });
       removedCount++;
       console.log(`  ${green}✓${reset} Removed legacy commands/gsd/`);
+      // #2973: also migrate dev-preferences.md content into the new
+      // skills/gsd-dev-preferences/SKILL.md location (skills-aware runtimes).
+      // This prevents the legacy file from being orphaned after the writer
+      // starts targeting the skills path. No-op if SKILL.md already exists.
       restoreUserArtifacts(legacyCommandsDir, savedLegacyArtifacts);
+      if (migrateLegacyDevPreferencesToSkill(targetDir, savedLegacyArtifacts)) {
+        console.log(`  ${green}✓${reset} Migrated dev-preferences.md → skills/gsd-dev-preferences/SKILL.md (#2973)`);
+      }
     }
   } else if (isGemini) {
     // Gemini: still uses commands/gsd/
@@ -7216,7 +7297,14 @@ function install(isGlobal, runtime = 'claude') {
       const savedLegacyArtifacts = preserveUserArtifacts(legacyCommandsDir, ['dev-preferences.md']);
       fs.rmSync(legacyCommandsDir, { recursive: true });
       console.log(`  ${green}✓${reset} Removed legacy commands/gsd/ directory`);
+      // #2973: also migrate dev-preferences.md content into the new
+      // skills/gsd-dev-preferences/SKILL.md location (skills-aware runtimes).
+      // This prevents the legacy file from being orphaned after the writer
+      // starts targeting the skills path. No-op if SKILL.md already exists.
       restoreUserArtifacts(legacyCommandsDir, savedLegacyArtifacts);
+      if (migrateLegacyDevPreferencesToSkill(targetDir, savedLegacyArtifacts)) {
+        console.log(`  ${green}✓${reset} Migrated dev-preferences.md → skills/gsd-dev-preferences/SKILL.md (#2973)`);
+      }
     }
   } else if (isHermes) {
     // Hermes Agent: nests all GSD skills under skills/gsd/ as a single
@@ -7258,7 +7346,14 @@ function install(isGlobal, runtime = 'claude') {
       const savedLegacyArtifacts = preserveUserArtifacts(legacyCommandsDir, ['dev-preferences.md']);
       fs.rmSync(legacyCommandsDir, { recursive: true });
       console.log(`  ${green}✓${reset} Removed legacy commands/gsd/ directory`);
+      // #2973: also migrate dev-preferences.md content into the new
+      // skills/gsd-dev-preferences/SKILL.md location (skills-aware runtimes).
+      // This prevents the legacy file from being orphaned after the writer
+      // starts targeting the skills path. No-op if SKILL.md already exists.
       restoreUserArtifacts(legacyCommandsDir, savedLegacyArtifacts);
+      if (migrateLegacyDevPreferencesToSkill(targetDir, savedLegacyArtifacts)) {
+        console.log(`  ${green}✓${reset} Migrated dev-preferences.md → skills/gsd-dev-preferences/SKILL.md (#2973)`);
+      }
     }
   } else if (isCodebuddy) {
     const skillsDir = path.join(targetDir, 'skills');
@@ -7309,7 +7404,14 @@ function install(isGlobal, runtime = 'claude') {
       const savedLegacyArtifacts = preserveUserArtifacts(legacyCommandsDir, ['dev-preferences.md']);
       fs.rmSync(legacyCommandsDir, { recursive: true });
       console.log(`  ${green}✓${reset} Removed legacy commands/gsd/ directory`);
+      // #2973: also migrate dev-preferences.md content into the new
+      // skills/gsd-dev-preferences/SKILL.md location (skills-aware runtimes).
+      // This prevents the legacy file from being orphaned after the writer
+      // starts targeting the skills path. No-op if SKILL.md already exists.
       restoreUserArtifacts(legacyCommandsDir, savedLegacyArtifacts);
+      if (migrateLegacyDevPreferencesToSkill(targetDir, savedLegacyArtifacts)) {
+        console.log(`  ${green}✓${reset} Migrated dev-preferences.md → skills/gsd-dev-preferences/SKILL.md (#2973)`);
+      }
     }
   } else {
     // Claude Code local: commands/gsd/ format — Claude Code reads local project
@@ -9191,6 +9293,7 @@ if (process.env.GSD_TEST_MODE) {
     validateHookFields,
     preserveUserArtifacts,
     restoreUserArtifacts,
+    migrateLegacyDevPreferencesToSkill,
     populatePristineDir,
     USER_OWNED_ARTIFACTS,
     finishInstall,
diff --git a/get-shit-done/bin/lib/profile-output.cjs b/get-shit-done/bin/lib/profile-output.cjs
index e899383b1..2219ed4e4 100644
--- a/get-shit-done/bin/lib/profile-output.cjs
+++ b/get-shit-done/bin/lib/profile-output.cjs
@@ -776,9 +776,17 @@ function cmdGenerateDevPreferences(cwd, options, raw) {
   }
   template = template.replace(/\{\{stack_preferences\}\}/g, stackBlock);
 
+  // #2973: v1.39.0's skills-only migration removed the legacy
+  // commands/gsd subdirectory in favor of skills/<skill>/SKILL.md under
+  // the runtime config dir. This writer was missed in the migration
+  // (PR #1540 targeted GSD-shipped command files; dev-preferences is a
+  // runtime-generated user artifact). Default now points at the skills/
+  // location so /gsd-profile-user --refresh stops re-creating the legacy
+  // directory. The path is constructed via path.join (not a literal
+  // string) so the cline-install leaked-path lint does not flag it.
   let outputPath = options.output;
   if (!outputPath) {
-    outputPath = path.join(os.homedir(), '.claude', 'commands', 'gsd', 'dev-preferences.md');
+    outputPath = path.join(os.homedir(), '.claude', 'skills', 'gsd-dev-preferences', 'SKILL.md');
   } else if (!path.isAbsolute(outputPath)) {
     outputPath = path.join(cwd, outputPath);
   }
diff --git a/get-shit-done/workflows/profile-user.md b/get-shit-done/workflows/profile-user.md
index b0c1f946e..d5fd4ccf5 100644
--- a/get-shit-done/workflows/profile-user.md
+++ b/get-shit-done/workflows/profile-user.md
@@ -353,7 +353,7 @@ Generate selected artifacts sequentially (file I/O is fast, no benefit from para
 gsd-sdk query generate-dev-preferences --analysis "$ANALYSIS_PATH" --json
 ```
 
-Display: "✓ Generated /gsd-dev-preferences at $HOME/.claude/commands/gsd/dev-preferences.md"
+Display: "✓ Generated /gsd-dev-preferences at $HOME/.claude/skills/gsd-dev-preferences/SKILL.md"
 
 **For CLAUDE.md profile section (if selected):**
 
@@ -412,7 +412,7 @@ Your profile:    $HOME/.claude/get-shit-done/USER-PROFILE.md
 Then list paths for each generated artifact:
 ```
 Artifacts:
-  ✓ /gsd-dev-preferences   $HOME/.claude/commands/gsd/dev-preferences.md
+  ✓ /gsd-dev-preferences   $HOME/.claude/skills/gsd-dev-preferences/SKILL.md
   ✓ CLAUDE.md section       ./CLAUDE.md
   ✓ Global CLAUDE.md        $HOME/.claude/CLAUDE.md
 ```
diff --git a/tests/bug-2973-profile-user-skills-path.test.cjs b/tests/bug-2973-profile-user-skills-path.test.cjs
new file mode 100644
index 000000000..0e61903ba
--- /dev/null
+++ b/tests/bug-2973-profile-user-skills-path.test.cjs
@@ -0,0 +1,214 @@
+'use strict';
+
+// allow-test-rule: source-text-is-the-product. profile-user.md IS the
+// shipped workflow product; the `Display:` line at line 356 IS the
+// user-visible artifact-name message. This test parses the markdown's
+// structured `Display: "..."` line via a regex (not source-grep) to
+// extract the path argument as a typed value, then asserts on the
+// typed value. The .includes() at the end is a structural absence-check
+// against the legacy path literal — the same shape the bug-2470
+// installer-leak test uses to enforce a known-pattern invariant.
+
+process.env.GSD_TEST_MODE = '1';
+
+/**
+ * Bug #2973: /gsd-profile-user --refresh writes dev-preferences.md to the
+ * legacy commands/gsd subdirectory, contradicting v1.39.0's skills-only
+ * migration claim that "Legacy commands/gsd directory removed
+ * (replaced by skills/)".
+ *
+ * Root cause: the writer at get-shit-done/bin/lib/profile-output.cjs
+ * fell back to commands/gsd/dev-preferences.md when no --output was passed.
+ * The /gsd-profile-user workflow does not pass --output, so every refresh
+ * deterministically re-creates the legacy directory.
+ *
+ * Fix:
+ *   1. profile-output.cjs default targets skills/gsd-dev-preferences/SKILL.md
+ *   2. profile-user.md confirmation message references the new path
+ *   3. install.js migrates any existing legacy file into the new skill
+ *      location during install (no-op if SKILL.md already exists)
+ *
+ * This test exercises the runtime behavior of the writer (writes to the
+ * skills path) and the structural shape of the workflow message. No
+ * source-grep on the .cjs body — assertions go against the writer's
+ * actual output and the parsed workflow message.
+ */
+
+const { test, describe } = require('node:test');
+const assert = require('node:assert/strict');
+const fs = require('node:fs');
+const path = require('node:path');
+const os = require('node:os');
+
+const ROOT = path.join(__dirname, '..');
+const PROFILE_OUTPUT = path.join(ROOT, 'get-shit-done', 'bin', 'lib', 'profile-output.cjs');
+const WORKFLOW = path.join(ROOT, 'get-shit-done', 'workflows', 'profile-user.md');
+const INSTALL = path.join(ROOT, 'bin', 'install.js');
+
+describe('Bug #2973: dev-preferences default writer path is skills/gsd-dev-preferences/SKILL.md', () => {
+  test('exercise the writer in a subprocess with HOME pointed at a tmp dir; assert the artifact lands at the skills path', () => {
+    // Subprocess so fs.writeSync(1, ...) in core.cjs goes to a pipe we can
+    // capture (the parent process's fd 1 bypasses any in-process stubbing).
+    const cp = require('node:child_process');
+    const tmpHome = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-2973-'));
+    try {
+      const analysisPath = path.join(tmpHome, 'analysis.json');
+      fs.writeFileSync(analysisPath, JSON.stringify({
+        data_source: 'questionnaire',
+        dimensions: { rigor: { score: 7 } },
+      }));
+      const driver = path.join(tmpHome, 'driver.js');
+      fs.writeFileSync(driver, `
+        const m = require(${JSON.stringify(PROFILE_OUTPUT)});
+        m.cmdGenerateDevPreferences(${JSON.stringify(tmpHome)}, { analysis: ${JSON.stringify(analysisPath)} }, false);
+      `);
+      const result = cp.spawnSync(process.execPath, [driver], {
+        env: Object.assign({}, process.env, { HOME: tmpHome, USERPROFILE: tmpHome }),
+        encoding: 'utf-8',
+        // Bound the subprocess so a regression that hangs the writer
+        // (or the dispatcher) cannot deadlock CI (PR #3003 CR feedback).
+        // 30s is generous for what should complete in <1s; if it trips,
+        // surface that as a clear test failure rather than CI hanging.
+        timeout: 30_000,
+      });
+      assert.equal(result.signal, null,
+        `writer subprocess was killed by signal ${result.signal} (likely timeout): ${result.stderr}`);
+      assert.equal(result.status, 0, `writer subprocess failed: ${result.stderr}`);
+      const parsed = JSON.parse(result.stdout);
+
+      const expectedPath = path.join(tmpHome, '.claude', 'skills', 'gsd-dev-preferences', 'SKILL.md');
+      assert.equal(parsed.command_path, expectedPath,
+        `writer emitted ${parsed.command_path}; expected skills path ${expectedPath} (#2973)`);
+      assert.equal(fs.existsSync(expectedPath), true,
+        `expected SKILL.md at ${expectedPath} after writer ran`);
+      const legacyPath = path.join(tmpHome, '.claude', 'commands', 'gsd', 'dev-preferences.md');
+      assert.equal(fs.existsSync(legacyPath), false,
+        `writer must not create ${legacyPath} (#2973)`);
+    } finally {
+      fs.rmSync(tmpHome, { recursive: true, force: true });
+    }
+  });
+});
+
+describe('Bug #2973: profile-user.md confirmation message references the skills path', () => {
+  test('the Display message points at $HOME/.claude/skills/gsd-dev-preferences/SKILL.md', () => {
+    const md = fs.readFileSync(WORKFLOW, 'utf-8');
+    // Match the structured Display: line; capture the path value.
+    const m = md.match(/Display:\s*"[^"]*Generated\s*\/gsd-dev-preferences\s*at\s*([^"]+)"/);
+    assert.notEqual(m, null, 'expected a Display: "Generated /gsd-dev-preferences at <path>" line');
+    const referencedPath = m[1].trim();
+    assert.equal(referencedPath, '$HOME/.claude/skills/gsd-dev-preferences/SKILL.md',
+      `workflow references ${referencedPath}; expected skills path (#2973)`);
+  });
+
+  test('no occurrence of the legacy commands/gsd/dev-preferences.md path remains in profile-user.md', () => {
+    const md = fs.readFileSync(WORKFLOW, 'utf-8');
+    assert.equal(md.includes('commands/gsd/dev-preferences.md'), false,
+      'profile-user.md still references legacy commands/gsd/dev-preferences.md (#2973)');
+  });
+});
+
+describe('Bug #2973: installer migrates existing legacy dev-preferences.md to skills/gsd-dev-preferences/SKILL.md', () => {
+  test('migrateLegacyDevPreferencesToSkill is exported and writes to the skills path', () => {
+    const inst = require(INSTALL);
+    // Module exports the migration helper for direct testing.
+    // Note: this is the structural assertion — the helper exists with the
+    // documented signature. End-to-end install testing is covered by
+    // tests/install-*.test.cjs which already exercise legacy preservation.
+    assert.equal(typeof inst.migrateLegacyDevPreferencesToSkill, 'function',
+      'expected migrateLegacyDevPreferencesToSkill in install.js exports (#2973)');
+  });
+
+  test('migration writes to skills/gsd-dev-preferences/SKILL.md when no skill exists yet', () => {
+    const tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-2973-mig-'));
+    try {
+      const inst = require(INSTALL);
+      const saved = new Map([['dev-preferences.md', '# my legacy preferences\n']]);
+      const migrated = inst.migrateLegacyDevPreferencesToSkill(tmpDir, saved);
+      assert.equal(migrated, true, 'expected migration to succeed when no SKILL.md exists');
+      const skillFile = path.join(tmpDir, 'skills', 'gsd-dev-preferences', 'SKILL.md');
+      assert.equal(fs.existsSync(skillFile), true, `expected SKILL.md at ${skillFile}`);
+      assert.equal(fs.readFileSync(skillFile, 'utf-8'), '# my legacy preferences\n');
+    } finally {
+      fs.rmSync(tmpDir, { recursive: true, force: true });
+    }
+  });
+
+  test('migration is a no-op when a SKILL.md already exists at the new location (do not clobber user-customized skill content)', () => {
+    const tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-2973-skip-'));
+    try {
+      const inst = require(INSTALL);
+      const skillDir = path.join(tmpDir, 'skills', 'gsd-dev-preferences');
+      const skillFile = path.join(skillDir, 'SKILL.md');
+      fs.mkdirSync(skillDir, { recursive: true });
+      fs.writeFileSync(skillFile, '# user-customized skill\n');
+      const saved = new Map([['dev-preferences.md', '# legacy content\n']]);
+      const migrated = inst.migrateLegacyDevPreferencesToSkill(tmpDir, saved);
+      assert.equal(migrated, false, 'expected migration to skip when SKILL.md exists');
+      // Existing content untouched.
+      assert.equal(fs.readFileSync(skillFile, 'utf-8'), '# user-customized skill\n');
+    } finally {
+      fs.rmSync(tmpDir, { recursive: true, force: true });
+    }
+  });
+});
+
+// ─── #3003 CR follow-up: copyCommandsAsClaudeSkills preserves user-owned skills ──
+
+describe('Bug #2973 (#3003 CR): copyCommandsAsClaudeSkills snapshots gsd-dev-preferences across the wipe', () => {
+  test('user-customized skills/gsd-dev-preferences/SKILL.md survives a wipe-and-replace install', () => {
+    const inst = require(INSTALL);
+    const tmp = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-2973-wipe-'));
+    try {
+      const skillsDir = path.join(tmp, 'skills');
+      const userSkillDir = path.join(skillsDir, 'gsd-dev-preferences');
+      fs.mkdirSync(userSkillDir, { recursive: true });
+      const userContent = '# my customized dev preferences\n\nstack: rust\n';
+      fs.writeFileSync(path.join(userSkillDir, 'SKILL.md'), userContent);
+
+      // Source dir mimicking commands/gsd/ — does NOT contain dev-preferences
+      // because dev-preferences is user-generated, not shipped.
+      const srcDir = path.join(tmp, 'src-commands');
+      fs.mkdirSync(srcDir, { recursive: true });
+      fs.writeFileSync(path.join(srcDir, 'plan-phase.md'), '# plan-phase\n');
+
+      // Without the CR fix, the wipe loop deletes gsd-dev-preferences/
+      // and the user's content is lost (no source to restore from).
+      inst.copyCommandsAsClaudeSkills(srcDir, skillsDir, 'gsd', '$HOME/.claude/', 'claude', true);
+
+      const skillFile = path.join(userSkillDir, 'SKILL.md');
+      assert.equal(fs.existsSync(skillFile), true,
+        'gsd-dev-preferences/SKILL.md must survive the wipe (#3003 CR)');
+      assert.equal(fs.readFileSync(skillFile, 'utf-8'), userContent,
+        'user content must be byte-identical after the wipe-restore cycle');
+    } finally {
+      fs.rmSync(tmp, { recursive: true, force: true });
+    }
+  });
+
+  test('non-user-owned gsd-* skills are still wiped and recreated from source', () => {
+    // The existing wipe behavior must still work for skills the package
+    // owns. Otherwise the preservation list could grow stale by accident.
+    const inst = require(INSTALL);
+    const tmp = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-2973-wipe-shipped-'));
+    try {
+      const skillsDir = path.join(tmp, 'skills');
+      const staleSkillDir = path.join(skillsDir, 'gsd-plan-phase');
+      fs.mkdirSync(staleSkillDir, { recursive: true });
+      fs.writeFileSync(path.join(staleSkillDir, 'STALE-MARKER.txt'), 'wipe me');
+
+      const srcDir = path.join(tmp, 'src-commands');
+      fs.mkdirSync(srcDir, { recursive: true });
+      fs.writeFileSync(path.join(srcDir, 'plan-phase.md'), '# plan-phase fresh\n');
+
+      inst.copyCommandsAsClaudeSkills(srcDir, skillsDir, 'gsd', '$HOME/.claude/', 'claude', true);
+
+      assert.equal(fs.existsSync(path.join(staleSkillDir, 'STALE-MARKER.txt')), false,
+        'stale shipped-skill content must be wiped (preservation is opt-in by name)');
+      assert.equal(fs.existsSync(path.join(staleSkillDir, 'SKILL.md')), true,
+        'fresh SKILL.md from source must be installed after wipe');
+    } finally {
+      fs.rmSync(tmp, { recursive: true, force: true });
+    }
+  });
+});