A post-checkout git hook can handle this unfortunate situation.

  mkdir -p ~/.githooks
  git config --global core.hooksPath ~/.githooks

  cat > ~/.githooks/post-checkout <<'EOF'
  #!/usr/bin/env bash
  if [ -d .agents/skills ] && [ ! -e .claude/skills ]; then
      mkdir -p .claude
      ln -s ../.agents/skills .claude/skills
  fi
  EOF

  chmod +x ~/.githooks/post-checkout