docs: update PDF user guide template for v5.0.0

- Version: v3.3.0 → v5.0.0, Electron 40 → 41
- Home Screen: rewritten with 3-tier command center
- New sections: Cost/Token Tracking (#12), Git Worktree Isolation (#13)
- Themes: surface token note for light theme support
- Sections renumbered (14 Themes, 15 Shortcuts, 16 Troubleshooting)
- TOC updated with new entries

Co-Authored-By: Rooty

Author: Wintersta7e