Add quick reference guide and upgrade script

- docs/QUICK-REFERENCE.md: Comprehensive quick reference card with
  - All commands organized by category
  - Shell aliases
  - Key paths
  - PA flags
  - Autonomy levels
  - Troubleshooting tips
- automation/upgrade.sh: Version upgrade management
  - Check for available upgrades (git-aware)
  - Pre-upgrade backup creation
  - Migration runner for version upgrades
  - Post-upgrade validation
- Updated shell completions with 16 aliases total
- Test suite now covers 24 tests

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

automation/test-scripts.sh

@@ -129,7 +129,7 @@ else
 fi
 
 # Test automation bash scripts
-for script in install.sh daily-maintenance.sh backup.sh restore.sh clean.sh debug.sh mcp-status.sh; do
+for script in install.sh daily-maintenance.sh backup.sh restore.sh clean.sh debug.sh mcp-status.sh upgrade.sh; do
     if [[ -f "${AUTOMATION_DIR}/${script}" ]]; then
         if bash -n "${AUTOMATION_DIR}/${script}" 2>/dev/null; then
             pass "${script} syntax valid"