merge: incorporate origin/main into community-mode branch

Conflicts resolved:
- VERSION: keep 0.13.0.0 (branch > main's 0.12.12.0)
- package.json: same version resolution
- CHANGELOG.md: keep both entries — 0.13.0.0 on top, then 0.12.12.0/11.0/10.0
- scripts/gen-skill-docs.ts: keep resolvers-based architecture, drop main's
  inline Codex helper duplicates (already in scripts/resolvers/codex-helpers.ts)

Main brought in: security audit compliance (conditional telemetry, credential
cleanup, dead code removal), skill prefix choice, Codex filesystem boundary,
audit regression tests.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

setup

@@ -4,7 +4,7 @@ set -e
 
 if ! command -v bun >/dev/null 2>&1; then
   echo "Error: bun is required but not installed." >&2
-  echo "Install it: curl -fsSL https://bun.sh/install | bash" >&2
+  echo "Install it: curl -fsSL https://bun.sh/install | BUN_VERSION=1.3.10 bash" >&2
   exit 1
 fi
 
@@ -24,12 +24,14 @@ esac
 HOST="claude"
 LOCAL_INSTALL=0
 SKILL_PREFIX=1
+SKILL_PREFIX_FLAG=0
 while [ $# -gt 0 ]; do
   case "$1" in
     --host) [ -z "$2" ] && echo "Missing value for --host (expected claude, codex, kiro, or auto)" >&2 && exit 1; HOST="$2"; shift 2 ;;
     --host=*) HOST="${1#--host=}"; shift ;;
     --local) LOCAL_INSTALL=1; shift ;;
-    --no-prefix) SKILL_PREFIX=0; shift ;;
+    --prefix)    SKILL_PREFIX=1; SKILL_PREFIX_FLAG=1; shift ;;
+    --no-prefix) SKILL_PREFIX=0; SKILL_PREFIX_FLAG=1; shift ;;
     *) shift ;;
   esac
 done
@@ -39,6 +41,44 @@ case "$HOST" in
   *) echo "Unknown --host value: $HOST (expected claude, codex, kiro, or auto)" >&2; exit 1 ;;
 esac
 
+# ─── Resolve skill prefix preference ─────────────────────────
+# Priority: CLI flag > saved config > interactive prompt (or flat default for non-TTY)
+GSTACK_CONFIG="$SOURCE_GSTACK_DIR/bin/gstack-config"
+if [ "$SKILL_PREFIX_FLAG" -eq 0 ]; then
+  _saved_prefix="$("$GSTACK_CONFIG" get skill_prefix 2>/dev/null || true)"
+  if [ "$_saved_prefix" = "true" ]; then
+    SKILL_PREFIX=1
+  elif [ "$_saved_prefix" = "false" ]; then
+    SKILL_PREFIX=0
+  else
+    # No saved preference — prompt interactively (or default flat for non-TTY)
+    if [ -t 0 ]; then
+      echo ""
+      echo "Skill naming: how should gstack skills appear?"
+      echo ""
+      echo "  1) Short names: /qa, /ship, /review"
+      echo "     Recommended. Clean and fast to type."
+      echo ""
+      echo "  2) Namespaced: /gstack-qa, /gstack-ship, /gstack-review"
+      echo "     Use this if you run other skill packs alongside gstack to avoid conflicts."
+      echo ""
+      printf "Choice [1/2] (default: 1): "
+      read -r _prefix_choice </dev/tty 2>/dev/null || _prefix_choice=""
+      case "$_prefix_choice" in
+        2) SKILL_PREFIX=1 ;;
+        *) SKILL_PREFIX=0 ;;
+      esac
+    else
+      SKILL_PREFIX=0
+    fi
+    # Save the choice for future runs
+    "$GSTACK_CONFIG" set skill_prefix "$([ "$SKILL_PREFIX" -eq 1 ] && echo true || echo false)" 2>/dev/null || true
+  fi
+else
+  # Flag was passed explicitly — persist the choice
+  "$GSTACK_CONFIG" set skill_prefix "$([ "$SKILL_PREFIX" -eq 1 ] && echo true || echo false)" 2>/dev/null || true
+fi
+
 # --local: install to .claude/skills/ in the current working directory
 if [ "$LOCAL_INSTALL" -eq 1 ]; then
   if [ "$HOST" = "codex" ]; then
@@ -266,6 +306,38 @@ cleanup_old_claude_symlinks() {
   fi
 }
 
+# ─── Helper: remove old prefixed Claude skill symlinks ────────────────────────
+# Reverse migration: when switching from gstack- prefixed names to flat names,
+# clean up stale gstack-* symlinks that point into the gstack directory.
+cleanup_prefixed_claude_symlinks() {
+  local gstack_dir="$1"
+  local skills_dir="$2"
+  local removed=()
+  for skill_dir in "$gstack_dir"/*/; do
+    if [ -f "$skill_dir/SKILL.md" ]; then
+      skill_name="$(basename "$skill_dir")"
+      [ "$skill_name" = "node_modules" ] && continue
+      # Only clean up prefixed symlinks for dirs that AREN'T already prefixed
+      # (e.g., remove gstack-qa but NOT gstack-upgrade which is the real dir name)
+      case "$skill_name" in gstack-*) continue ;; esac
+      prefixed_target="$skills_dir/gstack-$skill_name"
+      # Only remove if it's a symlink pointing into gstack/
+      if [ -L "$prefixed_target" ]; then
+        link_dest="$(readlink "$prefixed_target" 2>/dev/null || true)"
+        case "$link_dest" in
+          gstack/*|*/gstack/*)
+            rm -f "$prefixed_target"
+            removed+=("gstack-$skill_name")
+            ;;
+        esac
+      fi
+    fi
+  done
+  if [ ${#removed[@]} -gt 0 ]; then
+    echo "  cleaned up prefixed symlinks: ${removed[*]}"
+  fi
+}
+
 # ─── Helper: link generated Codex skills into a skills parent directory ──
 # Installs from .agents/skills/gstack-* (the generated Codex-format skills)
 # instead of source dirs (which have Claude paths).
@@ -393,9 +465,11 @@ fi
 
 if [ "$INSTALL_CLAUDE" -eq 1 ]; then
   if [ "$SKILLS_BASENAME" = "skills" ]; then
-    # Clean up old unprefixed symlinks from previous installs
+    # Clean up stale symlinks from the opposite prefix mode
     if [ "$SKILL_PREFIX" -eq 1 ]; then
       cleanup_old_claude_symlinks "$SOURCE_GSTACK_DIR" "$INSTALL_SKILLS_DIR"
+    else
+      cleanup_prefixed_claude_symlinks "$SOURCE_GSTACK_DIR" "$INSTALL_SKILLS_DIR"
     fi
     link_claude_skill_dirs "$SOURCE_GSTACK_DIR" "$INSTALL_SKILLS_DIR"
     if [ "$LOCAL_INSTALL" -eq 1 ]; then
@@ -497,9 +571,9 @@ if [ "$INSTALL_CODEX" -eq 1 ]; then
 fi
 
 # 8. First-time welcome + legacy cleanup
-if [ ! -d "$HOME/.gstack" ]; then
-  mkdir -p "$HOME/.gstack"
+if [ ! -f "$HOME/.gstack/.welcome-seen" ]; then
   echo "  Welcome! Run /gstack-upgrade anytime to stay current."
+  touch "$HOME/.gstack/.welcome-seen"
 fi
 rm -f /tmp/gstack-latest-version