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* 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>
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