fix: top-level skill dirs so Claude discovers unprefixed names (#761)

* fix: top-level skill dirs so Claude discovers unprefixed names

Replace directory symlinks (gstack/qa → qa) with real directories
containing a SKILL.md symlink. Claude Code auto-prefixes skills nested
under a parent dir symlink, so /plan-ceo-review became "Unknown skill"
even with skill_prefix=false. Real dirs fix this.

Also syncs package.json version to match VERSION file and updates
test assertions to match the new mkdir + ln approach.

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

* docs: update symlink references to new top-level directory pattern

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

* test: regression tests for top-level skill directory structure

Verifies the invariant that setup/relink creates real directories (not
symlinks) at the top level, with SKILL.md symlinks inside. This prevents
Claude Code from auto-prefixing skills with gstack- when using --no-prefix.

Tests added:
- unprefixed skills must be real dirs with SKILL.md symlinks
- prefixed skills must also be real dirs with SKILL.md symlinks
- old directory symlinks get upgraded to real directories
- cleanup functions handle both old symlinks and new dir pattern
- link function removes old directory symlinks before mkdir

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

* test: namespace isolation tests for first install + mode switching

Verifies the core invariant: when you pick a prefix mode, ONLY that
mode's entries exist. Zero pollution from the other mode.

- first install --no-prefix: only flat names, zero gstack-* leaks
- first install --prefix: only gstack-* names, zero flat leaks
- non-TTY defaults to flat names
- switching prefix→no-prefix removes ALL gstack-* entries
- switching no-prefix→prefix removes ALL flat entries

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

* feat: upgrade migration system — versioned fix scripts for broken state

Adds gstack-upgrade/migrations/ directory with version-keyed bash scripts
that run automatically during /gstack-upgrade (Step 4.75, after ./setup).
Each script is idempotent and handles state fixes that setup alone can't
cover. First migration: v0.15.2.0.sh runs gstack-relink to fix stale
directory symlinks from pre-v0.15.2.0 installs.

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

* test: migration script validation + v0.15.2.0 end-to-end fix test

Tests that migration scripts are executable, parse without syntax errors,
follow the v{VERSION}.sh naming convention, and that v0.15.2.0 actually
fixes stale directory symlinks by converting them to real directories.

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

* docs: upgrade migration guide in CONTRIBUTING.md + CLAUDE.md pointer

CONTRIBUTING.md: new "Upgrade migrations" section documenting when and
how to add migration scripts for broken on-disk state.

CLAUDE.md: added note under vendored symlink awareness pointing to
CONTRIBUTING.md's migration section when worried about broken installs.

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

---------

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

test/gen-skill-docs.test.ts

@@ -1969,13 +1969,43 @@ describe('setup script validation', () => {
     expect(fnBody).toContain('gstack*');
   });
 
-  test('link_claude_skill_dirs creates relative symlinks', () => {
-    // Claude links should be relative: ln -snf "gstack/$dir_name"
-    // Uses dir_name (not skill_name) because symlink target must point to the physical directory
+  test('link_claude_skill_dirs creates real directories with absolute SKILL.md symlinks', () => {
+    // Claude links should be real directories with absolute SKILL.md symlinks
+    // to ensure Claude Code discovers them as top-level skills (not nested under gstack/)
     const fnStart = setupContent.indexOf('link_claude_skill_dirs()');
     const fnEnd = setupContent.indexOf('}', setupContent.indexOf('linked[@]}', fnStart));
     const fnBody = setupContent.slice(fnStart, fnEnd);
-    expect(fnBody).toContain('ln -snf "gstack/$dir_name"');
+    expect(fnBody).toContain('mkdir -p "$target"');
+    expect(fnBody).toContain('ln -snf "$gstack_dir/$dir_name/SKILL.md" "$target/SKILL.md"');
+  });
+
+  // REGRESSION: cleanup functions must handle both old symlinks AND new real-directory pattern
+  test('cleanup functions handle real directories with symlinked SKILL.md', () => {
+    // cleanup_old_claude_symlinks must detect and remove real dirs with SKILL.md symlinks
+    const cleanupOldStart = setupContent.indexOf('cleanup_old_claude_symlinks()');
+    const cleanupOldEnd = setupContent.indexOf('}', setupContent.indexOf('cleaned up old', cleanupOldStart));
+    const cleanupOldBody = setupContent.slice(cleanupOldStart, cleanupOldEnd);
+    expect(cleanupOldBody).toContain('-d "$old_target"');
+    expect(cleanupOldBody).toContain('-L "$old_target/SKILL.md"');
+    expect(cleanupOldBody).toContain('rm -rf "$old_target"');
+
+    // cleanup_prefixed_claude_symlinks must also handle the new pattern
+    const cleanupPrefixedStart = setupContent.indexOf('cleanup_prefixed_claude_symlinks()');
+    const cleanupPrefixedEnd = setupContent.indexOf('}', setupContent.indexOf('cleaned up prefixed', cleanupPrefixedStart));
+    const cleanupPrefixedBody = setupContent.slice(cleanupPrefixedStart, cleanupPrefixedEnd);
+    expect(cleanupPrefixedBody).toContain('-d "$prefixed_target"');
+    expect(cleanupPrefixedBody).toContain('-L "$prefixed_target/SKILL.md"');
+    expect(cleanupPrefixedBody).toContain('rm -rf "$prefixed_target"');
+  });
+
+  // REGRESSION: link function must upgrade old directory symlinks
+  test('link_claude_skill_dirs removes old directory symlinks before creating real dirs', () => {
+    const fnStart = setupContent.indexOf('link_claude_skill_dirs()');
+    const fnEnd = setupContent.indexOf('}', setupContent.indexOf('linked[@]}', fnStart));
+    const fnBody = setupContent.slice(fnStart, fnEnd);
+    // Must check for and remove old symlinks before mkdir
+    expect(fnBody).toContain('if [ -L "$target" ]');
+    expect(fnBody).toContain('rm -f "$target"');
   });
 
   test('setup supports --host auto|claude|codex|kiro', () => {