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>

.claude/commands/cli/mode/bug-diagnosis.md

@@ -0,0 +1,130 @@
+---
+name: bug-diagnosis
+description: Bug diagnosis and fix suggestions using CLI tools with specialized template
+argument-hint: "[--agent] [--tool codex|gemini|qwen] [--enhance] [--cd path] bug description"
+allowed-tools: SlashCommand(*), Bash(*), Task(*)
+---
+
+# CLI Mode: Bug Diagnosis (/cli:mode:bug-diagnosis)
+
+## Purpose
+
+Systematic bug diagnosis with root cause analysis template (`~/.claude/workflows/cli-templates/prompts/development/bug-diagnosis.txt`).
+
+**Tool Selection**:
+- **gemini** (default) - Best for bug diagnosis
+- **qwen** - Fallback when Gemini unavailable
+- **codex** - Alternative for complex bug analysis
+
+## Parameters
+
+- `--tool <gemini|qwen|codex>` - Tool selection (default: gemini)
+- `--agent` - Use cli-execution-agent for automated context discovery
+- `--enhance` - Enhance bug description with `/enhance-prompt`
+- `--cd "path"` - Target directory for focused diagnosis
+- `<bug-description>` (Required) - Bug description or error details
+
+## Tool Usage
+
+**Gemini** (Primary):
+```bash
+# Uses gemini by default, or specify explicitly
+--tool gemini
+```
+
+**Qwen** (Fallback):
+```bash
+--tool qwen
+```
+
+**Codex** (Alternative):
+```bash
+--tool codex
+```
+
+## Execution Flow
+
+### Standard Mode
+1. Parse tool selection (default: gemini)
+2. Optional: enhance with `/enhance-prompt`
+3. Detect directory from `--cd` or auto-infer
+4. Build command with bug-diagnosis template
+5. Execute diagnosis (read-only)
+6. Save to `.workflow/WFS-[id]/.chat/`
+
+### Agent Mode (`--agent`)
+
+Delegates to agent for intelligent diagnosis:
+
+```javascript
+Task(
+  subagent_type="cli-execution-agent",
+  description="Bug root cause diagnosis",
+  prompt=`
+    Task: ${bug_description}
+    Mode: bug-diagnosis
+    Tool: ${tool_flag || 'auto-select'}  // gemini|qwen|codex
+    Directory: ${cd_path || 'auto-detect'}
+    Template: bug-diagnosis
+
+    Agent responsibilities:
+    1. Context Discovery:
+       - Locate error traces and logs
+       - Find related code sections
+       - Identify data flow paths
+
+    2. CLI Command Generation:
+       - Build Gemini/Qwen/Codex command
+       - Include diagnostic context
+       - Apply bug-diagnosis.txt template
+
+    3. Execution & Output:
+       - Execute root cause analysis
+       - Generate fix suggestions
+       - Save to .workflow/.chat/
+  `
+)
+```
+
+## Core Rules
+
+- **Read-only**: Diagnoses bugs, does NOT modify code
+- **Template**: Uses `bug-diagnosis.txt` for root cause analysis
+- **Output**: Saves to `.workflow/WFS-[id]/.chat/`
+
+## CLI Command Templates
+
+**Gemini/Qwen** (default, diagnosis only):
+```bash
+cd [dir] && gemini -p "
+PURPOSE: [goal]
+TASK: Root cause analysis
+MODE: analysis
+CONTEXT: @**/*
+EXPECTED: Diagnosis, fix plan
+RULES: $(cat ~/.claude/workflows/cli-templates/prompts/development/bug-diagnosis.txt)
+"
+# Qwen: Replace 'gemini' with 'qwen'
+```
+
+**Codex** (diagnosis + potential fixes):
+```bash
+codex -C [dir] --full-auto exec "
+PURPOSE: [goal]
+TASK: Bug diagnosis
+MODE: analysis
+CONTEXT: @**/*
+EXPECTED: Diagnosis, fix suggestions
+RULES: $(cat ~/.claude/workflows/cli-templates/prompts/development/bug-diagnosis.txt)
+" -m gpt-5 --skip-git-repo-check -s danger-full-access
+```
+
+## Output
+
+- **With session**: `.workflow/WFS-[id]/.chat/bug-diagnosis-[timestamp].md`
+- **No session**: `.workflow/.scratchpad/bug-diagnosis-[desc]-[timestamp].md`
+
+## Notes
+
+- Template: `~/.claude/workflows/cli-templates/prompts/development/bug-diagnosis.txt`
+- See `intelligent-tools-strategy.md` for detailed tool usage