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-2808-skill-hyphen-name.test.cjs

@@ -34,9 +34,18 @@ const path = require('node:path');
 const { cleanup, createTempDir } = require('./helpers.cjs');
 
 const ROOT = path.join(__dirname, '..');
-const { convertClaudeCommandToClaudeSkill, copyCommandsAsClaudeSkills, skillFrontmatterName } =
+const { convertClaudeCommandToClaudeSkill, installRuntimeArtifacts, uninstallRuntimeArtifacts, skillFrontmatterName } =
   require(path.join(ROOT, 'bin', 'install.js'));
 
+const {
+  loadSkillsManifest,
+  resolveProfile,
+} = require(path.join(ROOT, 'get-shit-done', 'bin', 'lib', 'install-profiles.cjs'));
+
+// Full resolved profile — installs all available skills from the source dir
+const _manifest = loadSkillsManifest();
+const resolvedProfileFull = resolveProfile({ modes: [], manifest: _manifest });
+
 const WORKFLOWS_DIR = path.join(ROOT, 'get-shit-done', 'workflows');
 const COMMANDS_DIR = path.join(ROOT, 'commands', 'gsd');
 
@@ -150,8 +159,15 @@ describe('bug-2808: SKILL.md name: uses hyphen form', () => {
   test('generated autocomplete skill surface uses hyphen names without underscores', (t) => {
     const tmp = createTempDir('gsd-autocomplete-surface-');
     t.after(() => cleanup(tmp));
-    const skillsDir = path.join(tmp, 'skills');
-    copyCommandsAsClaudeSkills(COMMANDS_DIR, skillsDir, 'gsd', '$HOME/.claude/', 'claude', true);
+
+    // Use the real COMMANDS_DIR as the source via .gsd-source marker.
+    // installRuntimeArtifacts('claude', configDir, 'global') writes to
+    // configDir/skills/gsd-*/SKILL.md using the same converter as the shim did.
+    const configDir = path.join(tmp, 'config');
+    fs.mkdirSync(configDir, { recursive: true });
+    fs.writeFileSync(path.join(configDir, '.gsd-source'), COMMANDS_DIR + '\n');
+    installRuntimeArtifacts('claude', configDir, 'global', resolvedProfileFull);
+    const skillsDir = path.join(configDir, 'skills');
 
     // Don't filter the directory listing by `startsWith('gsd-')` — that
     // would silently hide exactly the kind of drift this test exists to