fix(3663): applySurface creates missing dest dirs (Codex P1-1)

Remove the fs.existsSync(dest) guard in applySurface so _syncGsdDir is
always called. _syncGsdDir already does mkdirSync(..., { recursive: true })
so the destination is created when absent — recovering partially-initialized
or user-deleted runtime config dirs. Also threads manifest through to
_syncGsdDir as optional 4th arg (used by P1-2 Hermes fix).

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

get-shit-done/bin/lib/surface.cjs

@@ -208,9 +208,7 @@ function applySurface(runtimeConfigDir, layout, manifest, clusterMap) {
   for (const kind of layout.kinds) {
     const staged = kind.stage(resolved);
     const dest = path.join(layout.configDir, kind.destSubpath);
-    if (fs.existsSync(dest)) {
-      _syncGsdDir(staged, dest, kind);
-    }
+    _syncGsdDir(staged, dest, kind, manifest);
   }
   return resolved;
 }
@@ -224,11 +222,16 @@ function applySurface(runtimeConfigDir, layout, manifest, clusterMap) {
  *   by copying recursively; remove dirs not in staged set. Preserves dirs not matching
  *   the prefix (user-owned skills).
  *
+ * For Hermes (empty prefix): uses manifest membership to discriminate GSD-owned vs
+ * user-owned dirs. GSD-owned = stem in manifest; removal targets = in manifest AND
+ * not in staged set. User-owned (not in manifest) are always preserved.
+ *
  * @param {string} stagedDir source (staged temp dir or original)
  * @param {string} destDir runtime destination
  * @param {import('./runtime-artifact-layout.cjs').ArtifactKind|'commands'|'agents'} kind
+ * @param {Map<string, string[]>} [manifest] optional; required for Hermes empty-prefix removal
  */
-function _syncGsdDir(stagedDir, destDir, kind) {
+function _syncGsdDir(stagedDir, destDir, kind, manifest) {
   if (!fs.existsSync(stagedDir)) return;
   fs.mkdirSync(destDir, { recursive: true });
 
@@ -256,22 +259,35 @@ function _syncGsdDir(stagedDir, destDir, kind) {
       }
     }
 
-    // Empty prefix = destSubpath is the GSD namespace (Hermes: skills/gsd/).
-    // With no prefix filter, we cannot safely distinguish GSD-owned from user-owned dirs,
-    // so we only remove dirs that match the prefix. When kindPrefix === '',
-    // startsWith('') is always true but we must guard: skip removal entirely if prefix is
-    // empty so user dirs under skills/gsd/ are preserved (Hermes user-skill safety).
-    if (kindPrefix !== '') {
-      // Remove prefix-matched dirs in dest that are not in staged set
-      const destEntries = fs.readdirSync(destDir);
-      for (const entry of destEntries) {
-        const entryPath = path.join(destDir, entry);
-        if (!fs.statSync(entryPath).isDirectory()) continue;
-        if (!entry.startsWith(kindPrefix)) continue; // preserve user-owned dirs
-        if (!stagedDirs.has(entry)) {
-          try { fs.rmSync(entryPath, { recursive: true, force: true }); } catch {}
-        }
+    // Removal: discriminator depends on prefix shape.
+    // Non-empty prefix: GSD namespace IS the prefix; remove prefix-matching dirs not in staged set.
+    // Empty prefix (Hermes): GSD-owned = stem in manifest (i.e. canonically-shipped GSD skill).
+    //                        User-owned skills not in manifest are preserved.
+    // No manifest available: be conservative, don't remove anything.
+    const canonicalStems = manifest
+      ? new Set([...manifest.keys()].filter(k => !k.startsWith('_calls_agents_')))
+      : null;
+
+    const destEntries = fs.readdirSync(destDir);
+    for (const entry of destEntries) {
+      const entryPath = path.join(destDir, entry);
+      if (!fs.statSync(entryPath).isDirectory()) continue;
+
+      let isGsdOwned;
+      if (kindPrefix !== '') {
+        isGsdOwned = entry.startsWith(kindPrefix);
+      } else if (canonicalStems) {
+        // Hermes: empty prefix, destSubpath is the namespace.
+        // GSD-owned iff the directory name (stem) appears in the canonical manifest.
+        isGsdOwned = canonicalStems.has(entry);
+      } else {
+        // No manifest available: be conservative, don't remove anything.
+        continue;
       }
+
+      if (!isGsdOwned) continue;           // preserve user-owned
+      if (stagedDirs.has(entry)) continue; // current GSD-owned, keep
+      try { fs.rmSync(entryPath, { recursive: true, force: true }); } catch {}
     }
   } else {
     // commands / agents kind: work with .md files

tests/surface-apply.test.cjs

@@ -202,6 +202,31 @@ describe('applySurface', () => {
     assert.ok(fs.existsSync(foreignDir), 'my-custom-skill dir should be preserved');
   });
 
+  test('applySurface recreates missing destination directories', (t) => {
+    // Fixture: layout configDir exists but the dest subdirectory for the kinds does NOT.
+    const base = createTempDir('gsd-surface-missing-dest-');
+    t.after(() => cleanup(base));
+    const runtimeConfigDir = base;
+    // Do NOT pre-create commands/gsd or agents — they are intentionally absent.
+    writeActiveProfile(runtimeConfigDir, 'core');
+    writeSurface(runtimeConfigDir, {
+      baseProfile: 'core',
+      disabledClusters: [],
+      explicitAdds: [],
+      explicitRemoves: [],
+    });
+    const manifest = loadSkillsManifest(REAL_COMMANDS_DIR);
+    const layout = resolveRuntimeArtifactLayout('claude', runtimeConfigDir, 'local');
+    applySurface(runtimeConfigDir, layout, manifest, CLUSTERS);
+
+    // commands/gsd must have been created and populated
+    const commandsDir = path.join(runtimeConfigDir, 'commands', 'gsd');
+    assert.ok(fs.existsSync(commandsDir), 'commands/gsd dir should be created even if initially absent');
+    const files = fs.readdirSync(commandsDir).filter(f => f.endsWith('.md'));
+    assert.ok(files.length > 0, 'commands/gsd should contain staged skill files');
+    assert.ok(files.includes('help.md'), 'help.md should be present after applySurface on missing dest');
+  });
+
   test('_syncGsdDir skills kind (hermes): preserves non-GSD user dir under skills/gsd/ when kindPrefix is empty', (t) => {
     const { _syncGsdDir } = require('../get-shit-done/bin/lib/surface.cjs');