fix(3659): applySurface prunes skill dirs on cluster disable (#3766)

* test(3659): add regression tests for applySurface skill-dir pruning on cluster disable

Tests that applySurface with claude global scope correctly prunes
~/.claude/skills/gsd-STEM/ dirs for disabled clusters, preserves
gsd-STEM dirs in enabled clusters, leaves non-gsd user dirs untouched,
and is idempotent across two consecutive calls.

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

* fix(3659): applySurface now prunes ~/.claude/skills/gsd-STEM/ on cluster disable

Root cause: surface.md directed the AI to use RUNTIME_CONFIG_DIR=~/.claude/skills
(the skills sub-directory) instead of the base Claude config dir (~/.claude).
When runtimeConfigDir=~/.claude/skills and scope=global, the layout computes
dest=~/.claude/skills/skills — the wrong target — so pruning never reached
the actual gsd-STEM dirs in ~/.claude/skills/.

Fix:
- surface.md: correct RUNTIME_CONFIG_DIR to use the base config dir (~/.claude),
  add explicit SCOPE=global, and update all path references in execution_context.
  Surface state file moves from ~/.claude/skills/.gsd-surface.json to
  ~/.claude/.gsd-surface.json, matching install/uninstall conventions.
- surface.cjs: extract pruneSkillDirs() as a shared helper (single point of truth
  for gsd-STEM dir removal). _syncGsdDir now delegates to it instead of having
  the ownership/prune logic inline. Export pruneSkillDirs for callers that need
  stand-alone pruning without a full applySurface pass.

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

* chore(3659): update changeset to reference PR #3766

* fix(3659): manifest-membership gate on pruneSkillDirs prevents user gsd-* dir data loss

Finding 1 (CRITICAL): the prefixed branch previously deleted any on-disk dir that
matched the 'gsd-' prefix and was not in retainedNames. A user-created gsd-mything/
would be silently destroyed. Fix: deletion now requires BOTH prefix match AND
manifest membership (stem present in manifest). Dirs that match the prefix but are
not manifest-known are preserved with a process.stderr warning so the user knows the
dir was kept.

Finding 2 (type guard): the Hermes (empty-prefix) branch passed manifest directly to
new Set([...manifest.keys()]) without verifying it is actually a Map. A truthy
non-Map would throw. Fix: safeManifest = (manifest instanceof Map) ? manifest : null,
used in both branches. Non-Map manifest triggers the same conservative
no-deletions path already used when manifest is absent.

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

* test(3659): counter-test for all-clusters-disabled + user gsd-* dir preservation

Finding 3: add test (e) that disables every cluster (Object.keys(CLUSTERS)) and
asserts three things:
  1. All GSD-owned skill dirs (gsd-explore/, gsd-help/) are removed.
  2. Non-gsd user dir (my-custom-skill/) is preserved.
  3. User-created gsd-mything/ (prefix match, not in manifest) is preserved —
     this is the critical regression guard for the Finding 1 data-loss fix.

Also update the existing _syncGsdDir skills-kind test in surface-apply.test.cjs to
pass a manifest that declares old-skill as GSD-owned. Without a manifest the new
conservative path correctly preserves all unknown gsd-* dirs, which broke the
pre-existing no-manifest assertion; supplying the manifest restores the expected
pruning behavior and documents the required calling contract.

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

* fix(3659): address pr-review-toolkit + codex review findings

- Collapse redundant if/else in _syncGsdDir
- Collapse duplicate canonicalStems branches in pruneSkillDirs
- Update stale module-header comment (config-dir root)
- Clarify dead isGsdOwned guard comment
- Log rmSync failures to stderr
- Add pruneSkillDirs to module-header Exports JSDoc
- Remove unused imports in bug-3659 test file

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

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

tests/runtime-artifact-layout-surface.test.cjs

@@ -196,10 +196,22 @@ describe('applySurface', () => {
     fs.writeFileSync(path.join(foreignDir, 'SKILL.md'), '# custom\n', 'utf8');
 
     const skillsKind = { kind: 'skills', destSubpath: 'skills', prefix: 'gsd-', stage: () => stagedDir };
-    _syncGsdDir(stagedDir, destDir, skillsKind);
+
+    // Build a minimal manifest that includes the GSD-owned stems so that the
+    // manifest-membership gate (Finding 1 fix) correctly identifies gsd-old-skill
+    // as GSD-owned and prunes it. Without a manifest the new code conservatively
+    // preserves all gsd-* dirs it cannot confirm are GSD-owned.
+    const manifest = new Map([
+      ['help', []],
+      ['update', []],
+      ['old-skill', []],  // GSD-owned stale stem — must be pruned when not in staged set
+    ]);
+
+    _syncGsdDir(stagedDir, destDir, skillsKind, manifest);
 
     assert.ok(fs.existsSync(path.join(destDir, stem1, 'SKILL.md')), 'gsd-help/SKILL.md should be copied');
     assert.ok(fs.existsSync(path.join(destDir, stem2, 'SKILL.md')), 'gsd-update/SKILL.md should be copied');
+    // stale gsd- dir removed (it's in the manifest so it is GSD-owned, but not in staged set)
     assert.ok(!fs.existsSync(staleDir), 'stale gsd-old-skill dir should be removed');
     assert.ok(fs.existsSync(foreignDir), 'my-custom-skill dir should be preserved');
   });