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/workflow/plan.md

@@ -41,7 +41,7 @@ The command performs comprehensive analysis through:
   - **Simple tasks** (≤3 modules): Direct CLI tools with intelligent path navigation and multi-round analysis
     ```bash
     # Analyze specific directory
-    ~/.claude/scripts/gemini-wrapper -C src/auth -p "
+    cd "src/auth" && ~/.claude/scripts/gemini-wrapper -p "
     PURPOSE: Analyze authentication patterns
     TASK: Review auth implementation for security patterns
     CONTEXT: Focus on JWT handling and user validation
@@ -106,7 +106,7 @@ The following pre_analysis steps are generated for agent execution:
     {
       "step": "analyze_patterns",
       "action": "Analyze codebase patterns and architecture using CLI tools with directory context",
-      "command": "bash(~/.claude/scripts/gemini-wrapper -C [target_directory] -p \"PURPOSE: Analyze existing patterns TASK: Identify implementation patterns for [task_type] CONTEXT: [planning_context] [dependency_context] EXPECTED: Pattern analysis and recommendations RULES: Focus on architectural consistency\")",
+      "command": "bash(cd \"[target_directory]\" && ~/.claude/scripts/gemini-wrapper -p \"PURPOSE: Analyze existing patterns TASK: Identify implementation patterns for [task_type] CONTEXT: [planning_context] [dependency_context] EXPECTED: Pattern analysis and recommendations RULES: Focus on architectural consistency\")",
       "output_to": "pattern_analysis",
       "on_error": "skip_optional"
     },