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/completions.bash

@@ -45,6 +45,12 @@ _claude_mcp_status() {
     COMPREPLY=($(compgen -W "--json" -- "${cur}"))
 }
 
+_claude_upgrade() {
+    local cur="${COMP_WORDS[COMP_CWORD]}"
+
+    COMPREPLY=($(compgen -W "--check --backup --apply --help" -- "${cur}"))
+}
+
 _claude_memory_add() {
     local cur="${COMP_WORDS[COMP_CWORD]}"
     local prev="${COMP_WORDS[COMP_CWORD-1]}"
@@ -80,6 +86,7 @@ complete -F _claude_log log-viewer.py
 complete -F _claude_debug debug.sh
 complete -F _claude_export session-export.py
 complete -F _claude_mcp_status mcp-status.sh
+complete -F _claude_upgrade upgrade.sh
 
 # Alias completions for convenience
 alias claude-validate='~/.claude/automation/validate-setup.sh'
@@ -98,7 +105,8 @@ alias claude-log='python3 ~/.claude/automation/log-viewer.py'
 alias claude-debug='~/.claude/automation/debug.sh'
 alias claude-export='python3 ~/.claude/automation/session-export.py'
 alias claude-mcp='~/.claude/automation/mcp-status.sh'
+alias claude-upgrade='~/.claude/automation/upgrade.sh'
 
 echo "Claude Code completions loaded. Available aliases:"
 echo "  claude-{validate,status,backup,restore,clean,memory-add,memory-list}"
-echo "  claude-{search,history,install,test,maintenance,log,debug,export,mcp}"
+echo "  claude-{search,history,install,test,maintenance,log,debug,export,mcp,upgrade}"