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/gemini/mode/plan.md

@@ -19,7 +19,7 @@ model: sonnet
 ### Key Features
 - **Gemini CLI Integration**: Utilizes Gemini CLI's deep codebase analysis for informed planning decisions
 
-**--cd Parameter Rule**: When `--cd` parameter is provided, always execute `cd [path] && gemini --all-files -p "prompt"` to ensure analysis occurs in the specified directory context.
+**--cd Parameter Rule**: When `--cd` parameter is provided, always execute `cd "[path]" && gemini --all-files -p "prompt"` to ensure analysis occurs in the specified directory context.
 
 ## Usage
 
@@ -44,7 +44,7 @@ gemini --all-files -p "$(cat ~/.claude/prompt-templates/plan.md)
 Planning Topic: [user_description]"
 
 # Directory-specific analysis  
-cd [directory] && gemini --all-files -p "$(cat ~/.claude/prompt-templates/plan.md)
+cd "[directory]" && gemini --all-files -p "$(cat ~/.claude/prompt-templates/plan.md)
 Planning Topic: [user_description]"
 ```