refactor: migrate prompt templates to standardized structure and enhance CLI command documentation

Template Migration:
- Move templates from .claude/prompt-templates/ to .claude/workflows/cli-templates/prompts/
- Rename and reorganize: bug-fix.md → development/bug-diagnosis.txt
- Rename and reorganize: code-analysis.md → analysis/code-execution-tracing.txt
- Rename and reorganize: plan.md → planning/architecture-planning.txt

CLI Command Enhancements:
- Add clear tool selection hierarchy (gemini primary, qwen fallback, codex alternative)
- Enhance analyze.md, chat.md with tool descriptions and agent context
- Enhance mode/code-analysis.md, mode/bug-diagnosis.md, mode/plan.md with Task() wrapper
- Add all necessary codex parameters (--skip-git-repo-check -s danger-full-access)
- Simplify descriptions while preserving core functionality

Agent Updates:
- Streamline cli-execution-agent.md (600→250 lines, -60%)
- Add complete templates reference for standalone usage
- Remove dependency on intelligent-tools-strategy.md

Reference Updates:
- Update test-task-generate.md template path references
- Delete duplicate bug-index.md
- All template paths now use ~/.claude/workflows/cli-templates/prompts/ format

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

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

Author: catlog22

.claude/agents/cli-execution-agent.md

@@ -9,142 +9,128 @@ allowed-tools: SlashCommand(*), Bash(*), TodoWrite(*), Read(*), Glob(*), Task(*)
 
 ## Purpose
 
-Quick codebase analysis using CLI tools. **Analysis only - does NOT modify code**.
+Quick codebase analysis using CLI tools. **Read-only - does NOT modify code**.
 
-**Intent**: Understand code patterns, architecture, and provide insights/recommendations
-**Supported Tools**: codex, gemini (default), qwen
-
-## Core Behavior
-
-1. **Read-Only Analysis**: This command ONLY analyzes code and provides insights
-2. **No Code Modification**: Results are recommendations and analysis reports
-3. **Template-Based**: Automatically selects appropriate analysis template
-4. **Smart Pattern Detection**: Infers relevant files based on analysis target
+**Tool Selection**:
+- **gemini** (default) - Best for code analysis
+- **qwen** - Fallback when Gemini unavailable
+- **codex** - Alternative for deep analysis
 
 ## Parameters
 
-- `--agent` - Use cli-execution-agent for automated context discovery (5-phase intelligent mode)
-- `--tool <codex|gemini|qwen>` - Tool selection (default: gemini, ignored in agent mode)
+- `--tool <gemini|qwen|codex>` - Tool selection (default: gemini)
+- `--agent` - Use cli-execution-agent for automated context discovery
 - `--enhance` - Use `/enhance-prompt` for context-aware enhancement
 - `<analysis-target>` - Description of what to analyze
 
-## Execution Flow
+## Tool Usage
+
+**Gemini** (Primary):
+```bash
+--tool gemini  # or omit (default)
+```
 
-### Standard Mode (Default)
+**Qwen** (Fallback):
+```bash
+--tool qwen
+```
 
+**Codex** (Alternative):
+```bash
+--tool codex
+```
+
+## Execution Flow
+
+### Standard Mode
 1. Parse tool selection (default: gemini)
-2. If `--enhance`: Execute `/enhance-prompt` first to expand user intent
-3. Auto-detect analysis type from keywords → select template
-4. Build command with auto-detected file patterns and `MODE: analysis`
-5. Execute analysis (read-only, no code changes)
-6. Return analysis report with insights and recommendations
+2. Optional: enhance with `/enhance-prompt`
+3. Auto-detect file patterns from keywords
+4. Build command with analysis template
+5. Execute analysis (read-only)
+6. Save results
 
-### Agent Mode (`--agent` flag)
+### Agent Mode (`--agent`)
 
-Delegate task to `cli-execution-agent` for intelligent execution with automated context discovery.
+Delegates to agent for intelligent analysis:
 
-**Agent invocation**:
 ```javascript
 Task(
   subagent_type="cli-execution-agent",
-  description="Analyze codebase with automated context discovery",
+  description="Codebase analysis",
   prompt=`
     Task: ${analysis_target}
     Mode: analyze
-    Tool Preference: ${tool_flag || 'auto-select'}
-    ${enhance_flag ? 'Enhance: true' : ''}
-
-    Agent will autonomously:
-    - Discover relevant files and patterns
-    - Build enhanced analysis prompt
-    - Select optimal tool and execute
-    - Route output to session/scratchpad
+    Tool: ${tool_flag || 'auto-select'}  // gemini|qwen|codex
+    Enhance: ${enhance_flag || false}
+
+    Agent responsibilities:
+    1. Context Discovery:
+       - Discover relevant files/patterns
+       - Identify analysis scope
+       - Build file context
+
+    2. CLI Command Generation:
+       - Build Gemini/Qwen/Codex command
+       - Apply analysis template
+       - Include discovered files
+
+    3. Execution & Output:
+       - Execute analysis
+       - Generate insights report
+       - Save to .workflow/.chat/ or .scratchpad/
   `
 )
 ```
 
-The agent handles all phases internally (understanding, discovery, enhancement, execution, routing).
+## Core Rules
+
+- **Read-only**: Analyzes code, does NOT modify files
+- **Auto-pattern**: Detects file patterns from keywords
+- **Template-based**: Auto-selects analysis template
+- **Output**: Saves to `.workflow/WFS-[id]/.chat/` or `.scratchpad/`
 
 ## File Pattern Auto-Detection
 
-Keywords trigger specific file patterns (each @ references one pattern):
+Keywords → file patterns:
 - "auth" → `@**/*auth* @**/*user*`
-- "component" → `@src/components/**/* @**/*.component.*`
+- "component" → `@src/components/**/*`
 - "API" → `@**/api/**/* @**/routes/**/*`
 - "test" → `@**/*.test.* @**/*.spec.*`
-- "config" → `@*.config.* @**/config/**/*`
 - Generic → `@src/**/*`
 
-For complex patterns, use `rg` or MCP tools to discover files first, then execute CLI with precise file references.
-
-## Command Template
+## CLI Command Templates
 
+**Gemini/Qwen**:
 ```bash
 cd . && gemini -p "
-PURPOSE: [analysis goal from target]
-TASK: [auto-detected analysis type]
+PURPOSE: [goal]
+TASK: [analysis type]
 MODE: analysis
-CONTEXT: @CLAUDE.md [auto-detected file patterns]
-EXPECTED: Insights, patterns, recommendations (NO code modification)
-RULES: [auto-selected template] | Focus on [analysis aspect]
+CONTEXT: @CLAUDE.md [auto-detected patterns]
+EXPECTED: Insights, recommendations
+RULES: [auto-selected template]
 "
+# Qwen: Replace 'gemini' with 'qwen'
 ```
 
-## Examples
-
-**Basic Analysis (Standard Mode)**:
-```bash
-/cli:analyze "authentication patterns"
-# Executes: Gemini analysis with auth file patterns
-# Returns: Pattern analysis, architecture insights, recommendations
-```
-
-**Intelligent Analysis (Agent Mode)**:
+**Codex**:
 ```bash
-/cli:analyze --agent "authentication patterns"
-# Phase 1: Classifies intent=analyze, complexity=simple, keywords=['auth', 'patterns']
-# Phase 2: MCP discovers 12 auth files, identifies patterns
-# Phase 3: Builds enhanced prompt with discovered context
-# Phase 4: Executes Gemini with comprehensive file references
-# Phase 5: Saves execution log with all 5 phases documented
-# Returns: Comprehensive analysis + detailed execution log
-```
-
-**Architecture Analysis**:
-```bash
-/cli:analyze --tool qwen -p "component architecture"
-# Executes: Qwen with component file patterns
-# Returns: Architecture review, design patterns, improvement suggestions
-```
-
-**Performance Analysis**:
-```bash
-/cli:analyze --tool codex "performance bottlenecks"
-# Executes: Codex deep analysis with performance focus
-# Returns: Bottleneck identification, optimization recommendations
-```
-
-**Enhanced Analysis**:
-```bash
-/cli:analyze --enhance "fix auth issues"
-# Step 1: Enhance prompt to expand context
-# Step 2: Analysis with expanded context
-# Returns: Root cause analysis, fix recommendations (NO automatic fixes)
+codex -C . --full-auto exec "
+PURPOSE: [goal]
+TASK: [analysis type]
+MODE: analysis
+CONTEXT: @CLAUDE.md [patterns]
+EXPECTED: Deep insights
+RULES: [template]
+" -m gpt-5 --skip-git-repo-check -s danger-full-access
 ```
 
-## Output Routing
-
-**Output Destination Logic**:
-- **Active session exists AND analysis is session-relevant**:
-  - Save to `.workflow/WFS-[id]/.chat/analyze-[timestamp].md`
-- **No active session OR one-off analysis**:
-  - Save to `.workflow/.scratchpad/analyze-[description]-[timestamp].md`
+## Output
 
-**Examples**:
-- During active session `WFS-auth-system`, analyzing auth patterns → `.chat/analyze-20250105-143022.md`
-- No session, quick security check → `.scratchpad/analyze-security-20250105-143045.md`
+- **With session**: `.workflow/WFS-[id]/.chat/analyze-[timestamp].md`
+- **No session**: `.workflow/.scratchpad/analyze-[desc]-[timestamp].md`
 
 ## Notes
 
-- Command templates, file patterns, and best practices: see intelligent-tools-strategy.md (loaded in memory)
-- Scratchpad files can be promoted to workflow sessions if analysis proves valuable
+- See `intelligent-tools-strategy.md` for detailed tool usage and templates