install.sh

#!/usr/bin/env bash
# meta-analysis-skill — installer (symlink the skills into your agent)
#
# Symlinks (or copies) the five skills into your agent's skills directory so the
# agent discovers them. Run from anywhere after cloning the repo.
#
# This installs SKILLS only. For runtime DEPENDENCIES (R packages, node_modules,
# Python), run ./setup.sh first; verify with python3 doctor.py.
#
# Usage:
#   ./install.sh                       # symlink into ~/.claude/skills (default)
#   ./install.sh ~/.codex/skills       # symlink into a different agent's dir
#   ./install.sh ~/.claude/skills copy # copy instead of symlink
#
# The skills are interdependent: meta-analysis and systematic-review consume
# review-methodology-foundations (the SSOT base) by reference. Install all five.

set -euo pipefail

REPO_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
TARGET_DIR="${1:-$HOME/.claude/skills}"
MODE="${2:-symlink}"

SKILLS=(meta-analysis systematic-review review-methodology-foundations academic-ref-check manuscript-typeset)

echo "Installing ${#SKILLS[@]} skills → $TARGET_DIR  (mode: $MODE)"
mkdir -p "$TARGET_DIR"

for s in "${SKILLS[@]}"; do
  src="$REPO_DIR/skills/$s"
  dst="$TARGET_DIR/$s"
  if [ ! -d "$src" ]; then echo "  ! missing: $src — skipping"; continue; fi
  if [ -e "$dst" ] || [ -L "$dst" ]; then echo "  ~ exists, replacing: $dst"; rm -rf "$dst"; fi
  if [ "$MODE" = "copy" ]; then cp -R "$src" "$dst"; else ln -s "$src" "$dst"; fi
  echo "  ✓ $s"
done

echo ""
echo "Done. Next:"
echo "  • Dependencies:  ./setup.sh          # install R packages + node_modules + Python (one command)"
echo "  • Health check:  python3 doctor.py   # verify what is present / missing and what each gap costs"
echo "  • Then ask your agent for a meta-analysis or systematic review."