refactor(3664): migrate bin/install.js install/uninstall to Runtime Artifact Layout Module (#3674)

Phase 2 of #3660 / ADR-3660. Routes both lifecycle verbs through the
Runtime Artifact Layout Module landed in Phase 1 (#3663):

- Add installRuntimeArtifacts(runtime, configDir, scope, resolvedProfile)
  and uninstallRuntimeArtifacts(runtime, configDir, scope) as the public
  orchestrators. Both pre-prune stale gsd-* entries before staged copy;
  installRuntimeArtifacts brackets the prune+copy with preserveUserArtifacts /
  restoreUserArtifacts so user-owned content (e.g. gsd-dev-preferences) survives
  wipe-and-replace for claude/qwen/hermes runtimes.
- Add applyRuntimeContentRewritesInPlace as the per-runtime path/branding
  post-stage step (preserves byte-output equivalence with the legacy
  copyCommandsAs* pipeline, including Qwen/Hermes branding rewrites).
- Add _copyStaged, _removeGsdEntries kind-aware filesystem helpers.
- Add _runLegacyInstallMigrations, _runLegacyUninstallCleanup as thin
  dispatchers over existing ADR-0008 legacy migrations (Hermes flat->nested
  per #2841, dev-preferences-as-skill per #2973). For Hermes, also clean up
  the intermediate skills/gsd/gsd-*/ layout that pre-Phase-2 installs left
  on disk.
- Delete the 9 copyCommandsAs*Skills functions (Codex / Cursor / Windsurf /
  Trae / CodeBuddy / Copilot / Claude / Antigravity / Augment) and the
  _copyCommandsAsSkillsViaConverter helper. All test entry points migrated
  to call installRuntimeArtifacts directly through the unified seam.
- Collapse the 9-branch uninstall ladder to one uninstallRuntimeArtifacts
  call plus preserved non-layout side-effects (Codex TOML, Copilot
  instructions, hooks).
- Unify install dispatcher: a single _isSkillsRuntime gate routes all 11
  skills runtimes through installRuntimeArtifacts for both full and core/
  minimal profiles. Removes 11 per-runtime if-else branches (3 minimal-mode
  shim branches + 8 dead after-the-gate branches).

Net delta on bin/install.js: 11,495 -> 11,174 (-321 LOC).

New tests:
- tests/install-uninstall-layout-loop.test.cjs (34 tests) - per-runtime
  fixture assertions on install/uninstall/legacy-migration ordering.
- tests/install-hermes-regressions.test.cjs (6 tests) - covers the six
  defects surfaced by iterative review: Hermes upgrade leaves stale dirs,
  --hermes --profile=core fall-through, --qwen --profile=core fall-through,
  minimal-mode dev-preferences migration skipped (Hermes/Qwen/Claude-global),
  and ordering bug in _runLegacyInstallMigrations.

Existing tests (10,038 prior + 40 new) all green: 10,078/10,078 pass.

Refs #3664

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

tests/bug-1924-preserve-user-artifacts.test.cjs

@@ -170,21 +170,24 @@ describe('#1924: dev-preferences.md preserved across re-install (global Claude)'
     const originalContent = '# Dev Preferences\n\nI prefer TDD. I like short functions.\n';
     fs.writeFileSync(devPrefsPath, originalContent);
 
-    // Re-run installer (simulating gsd-update)
-    // Bug: this triggers legacy cleanup that rmSync's commands/gsd/ entirely,
-    // deleting dev-preferences.md
+    // Re-run installer (simulating gsd-update).
+    // In the layout-driven path (B2), legacy commands/gsd/ is removed and
+    // dev-preferences.md is migrated to skills/gsd-dev-preferences/SKILL.md (#2973).
     runInstaller(tmpDir);
 
+    // Content is migrated to the new canonical skills location (#2973).
+    // The old commands/gsd/ path is cleaned up; the skill file carries the content.
+    const devPrefSkillPath = path.join(tmpDir, 'skills', 'gsd-dev-preferences', 'SKILL.md');
     assert.ok(
-      fs.existsSync(devPrefsPath),
-      'dev-preferences.md must survive re-install — gsd-update legacy cleanup must not delete user-generated files'
+      fs.existsSync(devPrefSkillPath),
+      'dev-preferences.md must be migrated to skills/gsd-dev-preferences/SKILL.md — gsd-update legacy cleanup must not silently drop user-generated content'
     );
 
-    const afterContent = fs.readFileSync(devPrefsPath, 'utf8');
+    const afterContent = fs.readFileSync(devPrefSkillPath, 'utf8');
     assert.strictEqual(
       afterContent,
       originalContent,
-      'dev-preferences.md content must be identical after re-install'
+      'migrated dev-preferences content must be identical to the original'
     );
   });
 
@@ -199,19 +202,22 @@ describe('#1924: dev-preferences.md preserved across re-install (global Claude)'
     fs.writeFileSync(legacyFile, '---\nname: gsd:next\n---\n\nLegacy content.');
 
     // But dev-preferences.md is also there (user-generated)
+    const devPrefsContent = '# Dev Preferences\n\nMy preferences.\n';
     const devPrefsPath = path.join(commandsGsdDir, 'dev-preferences.md');
-    fs.writeFileSync(devPrefsPath, '# Dev Preferences\n\nMy preferences.\n');
+    fs.writeFileSync(devPrefsPath, devPrefsContent);
 
     // Re-install
     runInstaller(tmpDir);
 
-    // dev-preferences.md must be preserved
+    // In the layout-driven path (B2), commands/gsd/ is fully removed but
+    // dev-preferences.md content is migrated to the new canonical skill location.
+    const devPrefSkillPath = path.join(tmpDir, 'skills', 'gsd-dev-preferences', 'SKILL.md');
     assert.ok(
-      fs.existsSync(devPrefsPath),
-      'dev-preferences.md must be preserved while legacy commands/gsd/ is cleaned up'
+      fs.existsSync(devPrefSkillPath),
+      'dev-preferences.md content must be migrated to skills/gsd-dev-preferences/SKILL.md'
     );
 
-    // The legacy GSD command (next.md) is NOT user-generated, should be removed
+    // The legacy GSD command (next.md) is NOT user-generated, must be removed
     // (it would exist only as a skill now in skills/gsd-next/SKILL.md)
     assert.ok(
       !fs.existsSync(legacyFile),