feat: Update workflow architecture documentation and clean up scripts

- Update agent definitions with enhanced context and flow control
- Standardize command templates for consistent CLI tool integration
- Improve gemini-wrapper with better token management and path handling
- Simplify qwen-wrapper for streamlined execution
- Enhance intelligent-tools-strategy with directory navigation patterns
- Add proper quoting for Windows path compatibility in all commands
- Update workflow planning documentation with current architectural insights

These changes align the command system with the four-layer architecture
analysis and improve cross-platform compatibility.

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

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

.claude/commands/codex/mode/plan.md

@@ -15,7 +15,7 @@ model: sonnet
 
 ## Overview
 Comprehensive development planning and implementation strategy using expert planning templates with Codex CLI.
--   **Directory Analysis Rule**: When user intends to analyze specific directory (cd XXX), use: `codex --cd XXX --full-auto exec "prompt" -s danger-full-access` or `cd XXX && codex --full-auto exec "@{**/*} prompt" -s danger-full-access`
+-   **Directory Analysis Rule**: When user intends to analyze specific directory (cd XXX), use: `codex --cd XXX --full-auto exec "prompt" -s danger-full-access` or `cd "XXX" && codex --full-auto exec "@{**/*} prompt" -s danger-full-access`
 -   **Default Mode**: `--full-auto exec` autonomous development mode (RECOMMENDED for all tasks).