From 2dbf5504200322d8667016da03ffe75aaa066c75 Mon Sep 17 00:00:00 2001
From: catlog22 <catlog22@github.com>
Date: Sun, 5 Oct 2025 12:22:23 +0800
Subject: [PATCH] docs: clarify CLI command intent and add output routing
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- **Intent Clarification**: Distinguished analysis (read-only) from execution (modifies code) commands
- **Output Routing**: Added comprehensive output destination logic for all CLI commands
- **Scratchpad Integration**: Introduced `.workflow/.scratchpad/` for non-session-specific outputs

## Analysis Commands (Read-Only)
- `/cli:analyze`, `/cli:chat`, `/cli:mode:*`: Added "Core Behavior" emphasizing read-only nature
- Added "MODE: analysis" in command templates
- Examples clearly show recommendations vs. code changes

## Execution Commands (Modifies Code)
- `/cli:execute`: Added ⚠️ warnings about code modification
- `/cli:codex-execute`: Clarified multi-stage execution with detailed output structure
- Both commands now have "Output Routing" sections

## Workflow Architecture Updates
- Added `.workflow/.scratchpad/` directory definition
- Output routing logic: session-relevant → `.chat/`, otherwise → `.scratchpad/`
- File naming pattern: `[command-type]-[brief-description]-[timestamp].md`
- Examples for both analysis and implementation commands

## Key Improvements
- Prevents confusion between analysis and implementation operations
- Solves output loss when no active session exists
- Prevents unrelated analyses from cluttering session history
- Provides centralized location for ad-hoc outputs

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

Co-Authored-By: Claude <noreply@anthropic.com>
---
 .claude/commands/cli/analyze.md            |  76 +++++-
 .claude/commands/cli/chat.md               |  82 ++++++-
 .claude/commands/cli/codex-execute.md      |  46 +++-
 .claude/commands/cli/execute.md            | 122 ++++++++--
 .claude/commands/cli/mode/bug-index.md     |  87 +++++--
 .claude/commands/cli/mode/code-analysis.md |  98 ++++++--
 .claude/commands/cli/mode/plan.md          |  88 +++++--
 .claude/commands/workflow/tools/status.md  | 258 ---------------------
 .claude/workflows/workflow-architecture.md |  77 ++++--
 9 files changed, 556 insertions(+), 378 deletions(-)
 delete mode 100644 .claude/commands/workflow/tools/status.md

diff --git a/.claude/commands/cli/analyze.md b/.claude/commands/cli/analyze.md
index 331aa2fd..93f30007 100644
--- a/.claude/commands/cli/analyze.md
+++ b/.claude/commands/cli/analyze.md
@@ -14,10 +14,18 @@ allowed-tools: SlashCommand(*), Bash(*), TodoWrite(*), Read(*), Glob(*)
 
 ## Purpose
 
-Quick codebase analysis using CLI tools. Automatically detects analysis type and selects appropriate template.
+Quick codebase analysis using CLI tools. **Analysis 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
+
 ## Parameters
 
 - `--tool <codex|gemini|qwen>` - Tool selection (default: gemini)
@@ -29,8 +37,9 @@ Quick codebase analysis using CLI tools. Automatically detects analysis type and
 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
-5. Execute and return results
+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
 
 ## File Pattern Auto-Detection
 
@@ -44,17 +53,64 @@ Keywords trigger specific file patterns:
 
 For complex patterns, use `rg` or MCP tools to discover files first, then execute CLI with precise file references.
 
-## Examples
+## Command Template
 
 ```bash
-/cli:analyze "authentication patterns"              # Auto: gemini + auth patterns
-/cli:analyze --tool qwen "component architecture"   # Qwen architecture analysis
-/cli:analyze --tool codex "performance bottlenecks" # Codex deep analysis
-/cli:analyze --enhance "fix auth issues"            # Enhanced prompt → analysis
+cd . && ~/.claude/scripts/gemini-wrapper -p "
+PURPOSE: [analysis goal from target]
+TASK: [auto-detected 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]
+"
 ```
 
+## Examples
+
+**Basic Analysis**:
+```bash
+/cli:analyze "authentication patterns"
+# Executes: Gemini analysis with auth file patterns
+# Returns: Pattern analysis, architecture insights, recommendations
+```
+
+**Architecture Analysis**:
+```bash
+/cli:analyze --tool qwen "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)
+```
+
+## 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`
+
+**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`
+
 ## Notes
 
 - Command templates, file patterns, and best practices: see intelligent-tools-strategy.md (loaded in memory)
-- Active workflow session: results saved to `.workflow/WFS-[id]/.chat/`
-- No session: results returned directly
+- Scratchpad directory details: see workflow-architecture.md
+- Scratchpad files can be promoted to workflow sessions if analysis proves valuable
diff --git a/.claude/commands/cli/chat.md b/.claude/commands/cli/chat.md
index 6b163db4..479fd7c8 100644
--- a/.claude/commands/cli/chat.md
+++ b/.claude/commands/cli/chat.md
@@ -14,10 +14,18 @@ allowed-tools: SlashCommand(*), Bash(*)
 
 ## Purpose
 
-Direct Q&A interaction with CLI tools for codebase analysis.
+Direct Q&A interaction with CLI tools for codebase analysis. **Analysis only - does NOT modify code**.
 
+**Intent**: Ask questions, get explanations, understand codebase structure
 **Supported Tools**: codex, gemini (default), qwen
 
+## Core Behavior
+
+1. **Conversational Analysis**: Direct question-answer interaction about codebase
+2. **Read-Only**: This command ONLY provides information and analysis
+3. **No Code Modification**: Results are explanations and insights
+4. **Flexible Context**: Choose specific files or entire codebase
+
 ## Parameters
 
 - `<inquiry>` (Required) - Question or analysis request
@@ -31,8 +39,9 @@ Direct Q&A interaction with CLI tools for codebase analysis.
 1. Parse tool selection (default: gemini)
 2. If `--enhance`: Execute `/enhance-prompt` to expand user intent
 3. Assemble context: `@{CLAUDE.md}` + user-specified files or `--all-files`
-4. Execute CLI tool with assembled context
-5. Optionally save to workflow session
+4. Execute CLI tool with assembled context (read-only, analysis mode)
+5. Return explanations and insights (NO code changes)
+6. Optionally save to workflow session
 
 ## Context Assembly
 
@@ -44,18 +53,69 @@ Direct Q&A interaction with CLI tools for codebase analysis.
 
 For targeted analysis, use `rg` or MCP tools to discover relevant files first, then build precise CONTEXT field.
 
-## Examples
+## Command Template
 
 ```bash
-/cli:chat "analyze the authentication flow"              # Gemini (default)
-/cli:chat --tool qwen "optimize React component"         # Qwen
-/cli:chat --tool codex "review security vulnerabilities" # Codex
-/cli:chat --enhance "fix the login"                      # Enhanced prompt first
-/cli:chat --all-files "find all API endpoints"           # Full codebase context
+cd . && ~/.claude/scripts/gemini-wrapper -p "
+INQUIRY: [user question]
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [inferred or --all-files]
+MODE: analysis
+RESPONSE: Direct answer, explanation, insights (NO code modification)
+"
 ```
 
+## Examples
+
+**Basic Question**:
+```bash
+/cli:chat "analyze the authentication flow"
+# Executes: Gemini analysis
+# Returns: Explanation of auth flow, components involved, data flow
+```
+
+**Architecture Question**:
+```bash
+/cli:chat --tool qwen "how does React component optimization work here"
+# Executes: Qwen architecture analysis
+# Returns: Component structure explanation, optimization patterns used
+```
+
+**Security Analysis**:
+```bash
+/cli:chat --tool codex "review security vulnerabilities"
+# Executes: Codex security analysis
+# Returns: Vulnerability assessment, security recommendations (NO automatic fixes)
+```
+
+**Enhanced Inquiry**:
+```bash
+/cli:chat --enhance "explain the login issue"
+# Step 1: Enhance to expand login context
+# Step 2: Analysis with expanded understanding
+# Returns: Detailed explanation of login flow and potential issues
+```
+
+**Broad Context**:
+```bash
+/cli:chat --all-files "find all API endpoints"
+# Executes: Analysis across entire codebase
+# Returns: List and explanation of API endpoints (NO code generation)
+```
+
+## Output Routing
+
+**Output Destination Logic**:
+- **Active session exists AND query is session-relevant**:
+  - Save to `.workflow/WFS-[id]/.chat/chat-[timestamp].md`
+- **No active session OR unrelated query**:
+  - Save to `.workflow/.scratchpad/chat-[description]-[timestamp].md`
+
+**Examples**:
+- During active session `WFS-api-refactor`, asking about API structure → `.chat/chat-20250105-143022.md`
+- No session, asking about build process → `.scratchpad/chat-build-process-20250105-143045.md`
+
 ## Notes
 
 - Command templates and file patterns: see intelligent-tools-strategy.md (loaded in memory)
-- Active workflow session: results saved to `.workflow/WFS-[id]/.chat/`
-- No session: results returned directly
+- Scratchpad directory details: see workflow-architecture.md
+- Scratchpad conversations preserved for future reference
diff --git a/.claude/commands/cli/codex-execute.md b/.claude/commands/cli/codex-execute.md
index 31d99726..1fa1c32d 100644
--- a/.claude/commands/cli/codex-execute.md
+++ b/.claude/commands/cli/codex-execute.md
@@ -457,10 +457,45 @@ codex exec "CONTINUE TO NEXT SUBTASK: ..." resume --last --skip-git-repo-check -
 }
 ```
 
+## Output Routing
+
+**Execution Log Destination**:
+- **IF** active workflow session exists:
+  - Execution log: `.workflow/WFS-[id]/.chat/codex-execute-[timestamp].md`
+  - Task summaries: `.workflow/WFS-[id]/.summaries/[TASK-ID]-summary.md` (if task ID)
+  - Task updates: `.workflow/WFS-[id]/.task/[TASK-ID].json` status updates
+  - TodoWrite tracking: Embedded in execution log
+- **ELSE** (no active session):
+  - **Recommended**: Create workflow session first (`/workflow:session:start`)
+  - **Alternative**: Save to `.workflow/.scratchpad/codex-execute-[description]-[timestamp].md`
+
+**Output Files** (during execution):
+```
+.workflow/WFS-[session-id]/
+├── .chat/
+│   └── codex-execute-20250105-143022.md    # Full execution log with task flow
+├── .summaries/
+│   ├── IMPL-001.1-summary.md               # Subtask summaries
+│   ├── IMPL-001.2-summary.md
+│   └── IMPL-001-summary.md                 # Final task summary
+└── .task/
+    ├── IMPL-001.json                       # Updated task status
+    └── [subtask JSONs if decomposed]
+```
+
+**Examples**:
+- During session `WFS-auth-system`, executing multi-stage auth implementation:
+  - Log: `.workflow/WFS-auth-system/.chat/codex-execute-20250105-143022.md`
+  - Summaries: `.workflow/WFS-auth-system/.summaries/IMPL-001.{1,2,3}-summary.md`
+  - Task status: `.workflow/WFS-auth-system/.task/IMPL-001.json` (status: completed)
+- No session, ad-hoc multi-stage task:
+  - Log: `.workflow/.scratchpad/codex-execute-auth-refactor-20250105-143045.md`
+
 **Save Results**:
-- Execution log: `.chat/codex-execute-[timestamp].md` (if workflow active)
-- Summary: `.summaries/[TASK-ID]-summary.md` (if task ID provided)
-- TodoWrite tracking embedded in session
+- Execution log with task flow diagram and TodoWrite tracking
+- Individual summaries for each completed subtask
+- Final consolidated summary when all subtasks complete
+- Modified code files throughout project
 
 ## Notes
 
@@ -471,3 +506,8 @@ codex exec "CONTINUE TO NEXT SUBTASK: ..." resume --last --skip-git-repo-check -
 **Input Flexibility**: Accepts both freeform descriptions and task IDs (auto-detects and loads JSON)
 
 **Context Window**: `codex exec "..." resume --last` maintains conversation history, ensuring consistency across subtasks without redundant context injection.
+
+**Output Details**:
+- Output routing and scratchpad details: see workflow-architecture.md
+- Session management: see intelligent-tools-strategy.md
+- **⚠️ Code Modification**: This command performs multi-stage code modifications - execution log tracks all changes
diff --git a/.claude/commands/cli/execute.md b/.claude/commands/cli/execute.md
index 7cc67606..e79b5007 100644
--- a/.claude/commands/cli/execute.md
+++ b/.claude/commands/cli/execute.md
@@ -15,15 +15,25 @@ allowed-tools: SlashCommand(*), Bash(*)
 
 ## Purpose
 
-Execute implementation tasks with **YOLO permissions** (auto-approves all confirmations).
+Execute implementation tasks with **YOLO permissions** (auto-approves all confirmations). **MODIFIES CODE**.
 
+**Intent**: Autonomous code implementation, modification, and generation
 **Supported Tools**: codex, gemini (default), qwen
 **Key Feature**: Automatic context inference and file pattern detection
 
+## Core Behavior
+
+1. **Code Modification**: This command MODIFIES, CREATES, and DELETES code files
+2. **Auto-Approval**: YOLO mode bypasses confirmation prompts for all operations
+3. **Implementation Focus**: Executes actual code changes, not just recommendations
+4. **Requires Explicit Intent**: Use only when implementation is intended
+
 ## Core Concepts
 
 ### YOLO Permissions
-Auto-approves: file pattern inference, execution, file modifications, summary generation
+Auto-approves: file pattern inference, execution, **file modifications**, summary generation
+
+**⚠️ WARNING**: This command will make actual code changes without manual confirmation
 
 ### Execution Modes
 
@@ -70,30 +80,106 @@ Use `resume --last` when current task extends/relates to previous execution. See
 
 **Session Management**: Auto-detects `.workflow/.active-*` marker
 - Active session: Save to `.workflow/WFS-[id]/.chat/execute-[timestamp].md`
-- No session: Create new session
+- No session: Create new session or save to scratchpad
 
 **Task Integration**: Load from `.task/[TASK-ID].json`, update status, generate summary
 
-## Examples
+## Output Routing
+
+**Execution Log Destination**:
+- **IF** active workflow session exists:
+  - Save to `.workflow/WFS-[id]/.chat/execute-[timestamp].md`
+  - Update task status in `.task/[TASK-ID].json` (if task ID provided)
+  - Generate summary in `.workflow/WFS-[id]/.summaries/[TASK-ID]-summary.md`
+- **ELSE** (no active session):
+  - **Option 1**: Create new workflow session for task
+  - **Option 2**: Save to `.workflow/.scratchpad/execute-[description]-[timestamp].md`
+
+**Output Files** (when active session exists):
+- Execution log: `.workflow/WFS-[id]/.chat/execute-[timestamp].md`
+- Task summary: `.workflow/WFS-[id]/.summaries/[TASK-ID]-summary.md` (if task ID)
+- Modified code: Project files per implementation
+
+**Examples**:
+- During session `WFS-auth-system`, executing `IMPL-001`:
+  - Log: `.workflow/WFS-auth-system/.chat/execute-20250105-143022.md`
+  - Summary: `.workflow/WFS-auth-system/.summaries/IMPL-001-summary.md`
+- No session, ad-hoc implementation:
+  - Log: `.workflow/.scratchpad/execute-jwt-auth-20250105-143045.md`
+
+## Command Template
 
 ```bash
-# Description mode with auto-detection
-/cli:execute "implement JWT authentication with middleware"
+# Gemini/Qwen: MODE=write with --approval-mode yolo
+cd . && ~/.claude/scripts/gemini-wrapper --approval-mode yolo -p "
+PURPOSE: [implementation goal]
+TASK: [specific implementation]
+MODE: write
+CONTEXT: @{CLAUDE.md} [auto-detected files]
+EXPECTED: Working implementation with code changes
+RULES: [constraints] | Auto-approve all changes
+"
 
-# Enhanced prompt
-/cli:execute --enhance "implement JWT authentication"
-
-# Task ID mode
-/cli:execute IMPL-001
-
-# Codex execution
-/cli:execute --tool codex "optimize database queries"
-
-# Qwen with enhancement
-/cli:execute --tool qwen --enhance "refactor auth module"
+# Codex: MODE=auto with danger-full-access
+codex -C . --full-auto exec "
+PURPOSE: [implementation goal]
+TASK: [specific implementation]
+MODE: auto
+CONTEXT: [auto-detected files]
+EXPECTED: Complete implementation with tests
+" --skip-git-repo-check -s danger-full-access
 ```
 
+## Examples
+
+**Basic Implementation** (⚠️ modifies code):
+```bash
+/cli:execute "implement JWT authentication with middleware"
+# Executes: Creates auth middleware, updates routes, modifies config
+# Result: NEW/MODIFIED code files with JWT implementation
+```
+
+**Enhanced Implementation** (⚠️ modifies code):
+```bash
+/cli:execute --enhance "implement JWT authentication"
+# Step 1: Enhance to expand requirements
+# Step 2: Execute implementation with auto-approval
+# Result: Complete auth system with MODIFIED code files
+```
+
+**Task Execution** (⚠️ modifies code):
+```bash
+/cli:execute IMPL-001
+# Reads: .task/IMPL-001.json for requirements
+# Executes: Implementation based on task spec
+# Result: Code changes per task definition
+```
+
+**Codex Implementation** (⚠️ modifies code):
+```bash
+/cli:execute --tool codex "optimize database queries"
+# Executes: Codex with full file access
+# Result: MODIFIED query code, new indexes, updated tests
+```
+
+**Qwen Code Generation** (⚠️ modifies code):
+```bash
+/cli:execute --tool qwen --enhance "refactor auth module"
+# Step 1: Enhanced refactoring plan
+# Step 2: Execute with MODE=write
+# Result: REFACTORED auth code with structural changes
+```
+
+## Comparison with Analysis Commands
+
+| Command | Intent | Code Changes | Auto-Approve |
+|---------|--------|--------------|--------------|
+| `/cli:analyze` | Understand code | ❌ NO | N/A |
+| `/cli:chat` | Ask questions | ❌ NO | N/A |
+| `/cli:execute` | **Implement** | ✅ **YES** | ✅ **YES** |
+
 ## Notes
 
 - Command templates, YOLO mode details, and session management: see intelligent-tools-strategy.md (loaded in memory)
-- Auto-generated outputs: `.summaries/[TASK-ID]-summary.md`, `.chat/execute-[timestamp].md`
+- Output routing and scratchpad details: see workflow-architecture.md
+- **⚠️ Code Modification**: This command modifies code - execution logs document changes made
diff --git a/.claude/commands/cli/mode/bug-index.md b/.claude/commands/cli/mode/bug-index.md
index 85676d47..4728ab57 100644
--- a/.claude/commands/cli/mode/bug-index.md
+++ b/.claude/commands/cli/mode/bug-index.md
@@ -28,33 +28,66 @@ Systematic bug analysis with diagnostic template (`~/.claude/prompt-templates/bu
 
 ## Execution Flow
 
-1. Parse tool and directory options
-2. If `--enhance`: Execute `/enhance-prompt` to expand bug context
-3. Use bug-fix template: `~/.claude/prompt-templates/bug-fix.md`
-4. Execute with `--all-files` in target directory
-5. Save to `.workflow/WFS-[id]/.chat/bug-index-[timestamp].md`
+1. **Parse tool selection**: Extract `--tool` flag (default: gemini)
+2. **If `--enhance` flag present**: Execute `/enhance-prompt "[bug-description]"` first
+3. Parse bug description (original or enhanced)
+4. Detect target directory (from `--cd` or auto-infer)
+5. Build command for selected tool with bug-fix template
+6. Execute analysis (read-only, provides fix recommendations)
+7. Save to `.workflow/WFS-[id]/.chat/bug-index-[timestamp].md`
+
+## Core Rules
+
+1. **Analysis Only**: This command analyzes bugs and suggests fixes - it does NOT modify code
+2. **Enhance First (if flagged)**: Execute `/enhance-prompt` before analysis
+3. **Directory Context**: Use `cd` when `--cd` provided or auto-detected
+4. **Template Required**: Always use bug-fix template
+5. **Session Output**: Save analysis results and fix recommendations to session chat
 
 ## Analysis Focus (via Template)
 
-- Root cause investigation
-- Code path tracing
-- Targeted minimal fixes
-- Impact assessment
+- Root cause investigation and diagnosis
+- Code path tracing to locate issues
+- Targeted minimal fix recommendations
+- Impact assessment of proposed changes
+
+## Command Template
+
+```bash
+cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: [bug analysis goal]
+TASK: Systematic bug analysis and fix recommendations
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+EXPECTED: Root cause analysis, code path tracing, targeted fix suggestions
+RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: [description]
+"
+```
 
 ## Examples
 
+**Basic Bug Analysis**:
 ```bash
-# Basic bug analysis
-/cli:mode:bug-index "null pointer in authentication"
+cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: Debug authentication null pointer error
+TASK: Identify root cause and provide fix recommendations
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+EXPECTED: Root cause, code path, minimal fix suggestion, impact assessment
+RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: null pointer in login flow
+"
+```
 
-# Directory-specific
-/cli:mode:bug-index --cd "src/auth" "token validation fails"
-
-# Enhanced description
-/cli:mode:bug-index --enhance "login broken"
-
-# Qwen for architecture-related bugs
-/cli:mode:bug-index --tool qwen "circular dependency in modules"
+**Directory-Specific**:
+```bash
+cd src/auth && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: Fix token validation failure
+TASK: Analyze token validation bug in auth module
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+EXPECTED: Validation logic analysis, fix recommendation with minimal changes
+RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: token validation fails intermittently
+"
 ```
 
 ## Bug Investigation Workflow
@@ -62,13 +95,27 @@ Systematic bug analysis with diagnostic template (`~/.claude/prompt-templates/bu
 ```bash
 # 1. Find bug-related files
 rg "error_keyword" --files-with-matches
+mcp__code-index__search_code_advanced(pattern="error|exception", file_pattern="*.ts")
 
-# 2. Execute bug analysis with focused context
+# 2. Execute bug analysis with focused context (analysis only, no code changes)
 /cli:mode:bug-index --cd "src/module" "specific error description"
 ```
 
+## Output Routing
+
+**Output Destination Logic**:
+- **Active session exists AND bug is session-relevant**:
+  - Save to `.workflow/WFS-[id]/.chat/bug-index-[timestamp].md`
+- **No active session OR quick debugging**:
+  - Save to `.workflow/.scratchpad/bug-index-[description]-[timestamp].md`
+
+**Examples**:
+- During active session `WFS-payment-fix`, analyzing payment bug → `.chat/bug-index-20250105-143022.md`
+- No session, quick null pointer investigation → `.scratchpad/bug-index-null-pointer-20250105-143045.md`
+
 ## Notes
 
 - Command templates and file patterns: see intelligent-tools-strategy.md (loaded in memory)
+- Scratchpad directory details: see workflow-architecture.md
 - Template path: `~/.claude/prompt-templates/bug-fix.md`
 - Always uses `--all-files` for comprehensive codebase context
diff --git a/.claude/commands/cli/mode/code-analysis.md b/.claude/commands/cli/mode/code-analysis.md
index 43441f07..55b335b3 100644
--- a/.claude/commands/cli/mode/code-analysis.md
+++ b/.claude/commands/cli/mode/code-analysis.md
@@ -28,48 +28,100 @@ Systematic code analysis with execution path tracing template (`~/.claude/prompt
 
 ## Execution Flow
 
-1. Parse tool and directory options
-2. If `--enhance`: Execute `/enhance-prompt` to expand analysis intent
-3. Use code-analysis template: `~/.claude/prompt-templates/code-analysis.md`
-4. Execute with `--all-files` in target directory
-5. Save to `.workflow/WFS-[id]/.chat/code-analysis-[timestamp].md`
+1. **Parse tool selection**: Extract `--tool` flag (default: gemini)
+2. **If `--enhance` flag present**: Execute `/enhance-prompt "[analysis-target]"` first
+3. Parse analysis target (original or enhanced)
+4. Detect target directory (from `--cd` or auto-infer)
+5. Build command for selected tool with code-analysis template
+6. Execute deep analysis (read-only, no code modification)
+7. Save to `.workflow/WFS-[id]/.chat/code-analysis-[timestamp].md`
+
+## Core Rules
+
+1. **Analysis Only**: This command analyzes code and provides insights - it does NOT modify code
+2. **Tool Selection**: Use `--tool` value or default to gemini
+3. **Enhance First (if flagged)**: Execute `/enhance-prompt` before analysis
+4. **Directory Context**: Use `cd` when `--cd` provided or auto-detected
+5. **Template Required**: Always use code-analysis template
+6. **Session Output**: Save analysis results to session chat
 
 ## Analysis Capabilities (via Template)
 
-- Execution path tracing with variable states
-- Call flow visualization and diagrams
-- Control & data flow analysis
-- Logical reasoning ("why" behind code behavior)
-- Debugging insights and inefficiency detection
+- **Systematic Code Analysis**: Break down complex code into manageable parts
+- **Execution Path Tracing**: Track variable states and call stacks
+- **Control & Data Flow**: Understand code logic and data transformations
+- **Call Flow Visualization**: Diagram function calling sequences
+- **Logical Reasoning**: Explain "why" behind code behavior
+- **Debugging Insights**: Identify potential bugs or inefficiencies
+
+## Command Template
+
+```bash
+cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: [analysis goal]
+TASK: Systematic code analysis and execution path tracing
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+EXPECTED: Execution trace, call flow diagram, debugging insights
+RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on [aspect]
+"
+```
 
 ## Examples
 
+**Basic Code Analysis**:
 ```bash
-# Basic code analysis
-/cli:mode:code-analysis "trace authentication flow"
+cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: Trace authentication execution flow
+TASK: Analyze complete auth flow from request to response
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+EXPECTED: Step-by-step execution trace with call diagram, variable states
+RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on control flow
+"
+```
 
-# Directory-specific with enhancement
-/cli:mode:code-analysis --cd "src/auth" --enhance "how does JWT work"
-
-# Qwen for architecture analysis
-/cli:mode:code-analysis --tool qwen "explain microservices communication"
-
-# Codex for deep tracing
-/cli:mode:code-analysis --tool codex --cd "src/api" "trace request lifecycle"
+**Directory-Specific Analysis**:
+```bash
+cd src/auth && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: Understand JWT token validation logic
+TASK: Trace JWT validation from middleware to service layer
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+EXPECTED: Validation flow diagram, token lifecycle analysis
+RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on security
+"
 ```
 
 ## Code Tracing Workflow
 
 ```bash
-# 1. Find entry points
-rg "function.*main|export.*handler" --files-with-matches
+# 1. Find entry points and related files
+rg "function.*authenticate|class.*AuthService" --files-with-matches
+mcp__code-index__search_code_advanced(pattern="authenticate|login", file_pattern="*.ts")
 
-# 2. Execute deep analysis
+# 2. Build call graph understanding
+# entry → middleware → service → repository
+
+# 3. Execute deep analysis (analysis only, no code changes)
 /cli:mode:code-analysis --cd "src" "trace execution from entry point"
 ```
 
+## Output Routing
+
+**Output Destination Logic**:
+- **Active session exists AND analysis is session-relevant**:
+  - Save to `.workflow/WFS-[id]/.chat/code-analysis-[timestamp].md`
+- **No active session OR standalone analysis**:
+  - Save to `.workflow/.scratchpad/code-analysis-[description]-[timestamp].md`
+
+**Examples**:
+- During active session `WFS-auth-refactor`, analyzing auth flow → `.chat/code-analysis-20250105-143022.md`
+- No session, tracing request lifecycle → `.scratchpad/code-analysis-request-flow-20250105-143045.md`
+
 ## Notes
 
 - Command templates and file patterns: see intelligent-tools-strategy.md (loaded in memory)
+- Scratchpad directory details: see workflow-architecture.md
 - Template path: `~/.claude/prompt-templates/code-analysis.md`
 - Always uses `--all-files` for comprehensive code context
diff --git a/.claude/commands/cli/mode/plan.md b/.claude/commands/cli/mode/plan.md
index 8f30473d..1e78adfc 100644
--- a/.claude/commands/cli/mode/plan.md
+++ b/.claude/commands/cli/mode/plan.md
@@ -28,48 +28,98 @@ Comprehensive planning and architecture analysis with strategic planning templat
 
 ## Execution Flow
 
-1. Parse tool and directory options
-2. If `--enhance`: Execute `/enhance-prompt` to expand planning context
-3. Use planning template: `~/.claude/prompt-templates/plan.md`
-4. Execute with `--all-files` in target directory
-5. Save to `.workflow/WFS-[id]/.chat/plan-[timestamp].md`
+1. **Parse tool selection**: Extract `--tool` flag (default: gemini)
+2. **If `--enhance` flag present**: Execute `/enhance-prompt "[topic]"` first
+3. Parse topic (original or enhanced)
+4. Detect target directory (from `--cd` or auto-infer)
+5. Build command for selected tool with planning template
+6. Execute analysis (read-only, no code modification)
+7. Save to `.workflow/WFS-[id]/.chat/plan-[timestamp].md`
+
+## Core Rules
+
+1. **Analysis Only**: This command provides planning recommendations and insights - it does NOT modify code
+2. **Enhance First (if flagged)**: Execute `/enhance-prompt` before planning
+3. **Directory Context**: Use `cd` when `--cd` provided or auto-detected
+4. **Template Required**: Always use planning template
+5. **Session Output**: Save analysis results to session chat
 
 ## Planning Capabilities (via Template)
 
-- Strategic architecture insights
-- Implementation roadmaps
-- Key technical decisions
+- Strategic architecture insights and recommendations
+- Implementation roadmaps and suggestions
+- Key technical decisions analysis
 - Risk assessment
 - Resource planning
 
-## Examples
+## Command Template
 
 ```bash
-# Basic planning
-/cli:mode:plan "design user dashboard"
+cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: [planning goal from topic]
+TASK: Comprehensive planning and architecture analysis
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+EXPECTED: Strategic insights, implementation recommendations, key decisions
+RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on [topic area]
+"
+```
 
-# Enhanced with directory scope
-/cli:mode:plan --cd "src/api" --enhance "plan API refactoring"
+## Examples
 
-# Qwen for architecture planning
-/cli:mode:plan --tool qwen "plan microservices migration"
+**Basic Planning Analysis**:
+```bash
+cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: Design user dashboard architecture
+TASK: Plan dashboard component structure and data flow
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+EXPECTED: Architecture recommendations, component design, data flow diagram
+RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on scalability
+"
+```
 
-# Codex for technical planning
-/cli:mode:plan --tool codex "plan testing strategy"
+**Directory-Specific Planning**:
+```bash
+cd src/api && ~/.claude/scripts/gemini-wrapper --all-files -p "
+PURPOSE: Plan API refactoring strategy
+TASK: Analyze current API structure and recommend improvements
+MODE: analysis
+CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+EXPECTED: Refactoring roadmap, breaking change analysis, migration plan
+RULES: $(cat ~/.claude/prompt-templates/plan.md) | Maintain backward compatibility
+"
 ```
 
 ## Planning Workflow
 
 ```bash
-# 1. Gather existing architecture info
+# 1. Discover project structure
+~/.claude/scripts/get_modules_by_depth.sh
+mcp__code-index__find_files(pattern="*.ts")
+
+# 2. Gather existing architecture info
 rg "architecture|design" --files-with-matches
 
-# 2. Execute planning analysis
+# 3. Execute planning analysis (analysis only, no code changes)
 /cli:mode:plan "topic for strategic planning"
 ```
 
+## Output Routing
+
+**Output Destination Logic**:
+- **Active session exists AND planning is session-relevant**:
+  - Save to `.workflow/WFS-[id]/.chat/plan-[timestamp].md`
+- **No active session OR exploratory planning**:
+  - Save to `.workflow/.scratchpad/plan-[description]-[timestamp].md`
+
+**Examples**:
+- During active session `WFS-dashboard`, planning dashboard architecture → `.chat/plan-20250105-143022.md`
+- No session, exploring new feature idea → `.scratchpad/plan-feature-idea-20250105-143045.md`
+
 ## Notes
 
 - Command templates and file patterns: see intelligent-tools-strategy.md (loaded in memory)
+- Scratchpad directory details: see workflow-architecture.md
 - Template path: `~/.claude/prompt-templates/plan.md`
 - Always uses `--all-files` for comprehensive project context
diff --git a/.claude/commands/workflow/tools/status.md b/.claude/commands/workflow/tools/status.md
deleted file mode 100644
index 3d1da6f4..00000000
--- a/.claude/commands/workflow/tools/status.md
+++ /dev/null
@@ -1,258 +0,0 @@
----
-name: workflow:status
-description: Generate on-demand views from JSON task data
-usage: /workflow:status [task-id] [--format=<format>] [--validate]
-argument-hint: [optional: task-id, format, validation]
-examples:
-  - /workflow:status
-  - /workflow:status impl-1
-  - /workflow:status --format=hierarchy
-  - /workflow:status --validate
----
-
-# Workflow Status Command (/workflow:status)
-
-## Overview
-Generates on-demand views from JSON task data. No synchronization needed - all views are calculated from the current state of JSON files.
-
-## Core Principles
-**Data Source:** @~/.claude/workflows/workflow-architecture.md
-
-## Key Features
-
-### Pure View Generation
-- **No Sync**: Views are generated, not synchronized
-- **Always Current**: Reads latest JSON data every time
-- **No Persistence**: Views are temporary, not saved
-- **Single Source**: All data comes from JSON files only
-
-### Multiple View Formats
-- **Overview** (default): Current tasks and status
-- **Hierarchy**: Task relationships and structure
-- **Details**: Specific task information
-
-## Usage
-
-### Default Overview
-```bash
-/workflow:status
-```
-
-Generates current workflow overview:
-```markdown
-# Workflow Overview
-**Session**: WFS-user-auth
-**Phase**: IMPLEMENT
-**Type**: medium
-
-## Active Tasks
-- [⚠️] impl-1: Build authentication module (code-developer)
-- [⚠️] impl-2: Setup user management (code-developer)
-
-## Completed Tasks
-- [✅] impl-0: Project setup
-
-## Stats
-- **Total**: 8 tasks
-- **Completed**: 3
-- **Active**: 2
-- **Remaining**: 3
-```
-
-### Specific Task View
-```bash
-/workflow:status impl-1
-```
-
-Shows detailed task information:
-```markdown
-# Task: impl-1
-
-**Title**: Build authentication module
-**Status**: active
-**Agent**: @code-developer
-**Type**: feature
-
-## Context
-- **Requirements**: JWT authentication, OAuth2 support
-- **Scope**: src/auth/*, tests/auth/*
-- **Acceptance**: Module handles JWT tokens, OAuth2 flow implemented
-- **Inherited From**: WFS-user-auth
-
-## Relations
-- **Parent**: none
-- **Subtasks**: impl-1.1, impl-1.2
-- **Dependencies**: impl-0
-
-## Execution
-- **Attempts**: 0
-- **Last Attempt**: never
-
-## Metadata
-- **Created**: 2025-09-05T10:30:00Z
-- **Updated**: 2025-09-05T10:35:00Z
-```
-
-### Hierarchy View
-```bash
-/workflow:status --format=hierarchy
-```
-
-Shows task relationships:
-```markdown
-# Task Hierarchy
-
-## Main Tasks
-- impl-0: Project setup ✅
-- impl-1: Build authentication module ⚠️
-  - impl-1.1: Design auth schema
-  - impl-1.2: Implement auth logic
-- impl-2: Setup user management ⚠️
-
-## Dependencies
-- impl-1 → depends on → impl-0
-- impl-2 → depends on → impl-1
-```
-
-## View Generation Process
-
-### Data Loading
-```pseudo
-function generate_workflow_status(task_id, format):
-  // Load all current data
-  session = load_workflow_session()
-  all_tasks = load_all_task_json_files()
-
-  // Filter if specific task requested
-  if task_id:
-    target_task = find_task(all_tasks, task_id)
-    return generate_task_detail_view(target_task)
-
-  // Generate requested format
-  switch format:
-    case 'hierarchy':
-      return generate_hierarchy_view(all_tasks)
-    default:
-      return generate_overview(session, all_tasks)
-```
-
-### Real-Time Calculation
-- **Task Counts**: Calculated from JSON file status fields
-- **Relationships**: Built from JSON relations fields
-- **Status**: Read directly from current JSON state
-
-## Validation Mode
-
-### Basic Validation
-```bash
-/workflow:status --validate
-```
-
-Performs integrity checks:
-```markdown
-# Validation Results
-
-## JSON File Validation
-✅ All task JSON files are valid
-✅ Session file is valid and readable
-
-## Relationship Validation
-✅ All parent-child relationships are valid
-✅ All dependencies reference existing tasks
-✅ No circular dependencies detected
-
-## Hierarchy Validation
-✅ Task hierarchy within depth limits (max 3 levels)
-✅ All subtask references are bidirectional
-
-## Issues Found
-⚠️ impl-3: No subtasks defined (expected for leaf task)
-
-**Status**: All systems operational
-```
-
-### Validation Checks
-- **JSON Schema**: All files parse correctly
-- **References**: All task IDs exist
-- **Hierarchy**: Parent-child relationships are valid
-- **Dependencies**: No circular dependencies
-- **Depth**: Task hierarchy within limits
-
-## Error Handling
-
-### Missing Files
-```bash
-❌ Session file not found
-→ Initialize new workflow session? (y/n)
-
-❌ Task impl-5 not found
-→ Available tasks: impl-1, impl-2, impl-3, impl-4
-```
-
-### Invalid Data
-```bash
-❌ Invalid JSON in impl-2.json
-→ Cannot generate view for impl-2
-→ Repair file manually or recreate task
-
-⚠️ Circular dependency detected: impl-1 → impl-2 → impl-1
-→ Task relationships may be incorrect
-```
-
-## Performance Benefits
-
-### Fast Generation
-- **No File Writes**: Only reads JSON files
-- **No Sync Logic**: No complex synchronization
-- **Instant Results**: Generate views on demand
-- **No Conflicts**: No state consistency issues
-
-### Scalability
-- **Large Task Sets**: Handles hundreds of tasks efficiently
-- **Complex Hierarchies**: No performance degradation
-- **Concurrent Access**: Multiple views can be generated simultaneously
-
-## Integration
-
-### Workflow Integration
-- Use after task creation to see current state
-- Use for debugging task relationships
-
-### Command Integration
-```bash
-# Common workflow
-/task:create "New feature"
-/workflow:status                    # Check current state
-/task:breakdown impl-1
-/workflow:status --format=hierarchy # View new structure
-/task:execute impl-1.1
-```
-
-## Output Formats
-
-### Supported Formats
-- `overview` (default): General workflow status
-- `hierarchy`: Task relationships
-- `tasks`: Simple task list
-- `details`: Comprehensive information
-
-### Custom Filtering
-```bash
-# Show only active tasks
-/workflow:status --format=tasks --filter=active
-
-# Show completed tasks only
-/workflow:status --format=tasks --filter=completed
-
-# Show tasks for specific agent
-/workflow:status --format=tasks --agent=@code-developer
-```
-
-## Related Commands
-
-- `/task:create` - Create tasks (generates JSON data)
-- `/task:execute` - Execute tasks (updates JSON data)
-- `/task:breakdown` - Create subtasks (generates more JSON data)
-- `/workflow:vibe` - Coordinate agents (uses workflow status for coordination)
-
-This workflow status system provides instant, accurate views of workflow state without any synchronization complexity or performance overhead.
\ No newline at end of file
diff --git a/.claude/workflows/workflow-architecture.md b/.claude/workflows/workflow-architecture.md
index 8802a7b3..0d3d724e 100644
--- a/.claude/workflows/workflow-architecture.md
+++ b/.claude/workflows/workflow-architecture.md
@@ -266,28 +266,73 @@ All workflows use the same file structure definition regardless of complexity. *
 
 #### Complete Structure Reference
 ```
-.workflow/WFS-[topic-slug]/
-├── workflow-session.json        # Session metadata and state (REQUIRED)
-├── [.brainstorming/]           # Optional brainstorming phase (created when needed)
-├── [.chat/]                    # CLI interaction sessions (created when analysis is run)
-│   ├── chat-*.md              # Saved chat sessions
-│   └── analysis-*.md          # Analysis results
-├── [.process/]                 # Planning analysis results (created by /workflow:plan)
-│   └── ANALYSIS_RESULTS.md    # Analysis results and planning artifacts
-├── IMPL_PLAN.md                # Planning document (REQUIRED)
-├── TODO_LIST.md                # Progress tracking (REQUIRED)
-├── [.summaries/]               # Task completion summaries (created when tasks complete)
-│   ├── IMPL-*-summary.md      # Main task summaries
-│   └── IMPL-*.*-summary.md    # Subtask summaries
-└── .task/                      # Task definitions (REQUIRED)
-    ├── IMPL-*.json             # Main task definitions
-    └── IMPL-*.*.json           # Subtask definitions (created dynamically)
+.workflow/
+├── [.scratchpad/]              # Non-session-specific outputs (created when needed)
+│   ├── analyze-*-[timestamp].md        # One-off analysis results
+│   ├── chat-*-[timestamp].md           # Standalone chat sessions
+│   ├── plan-*-[timestamp].md           # Ad-hoc planning notes
+│   ├── bug-index-*-[timestamp].md      # Quick bug analyses
+│   ├── code-analysis-*-[timestamp].md  # Standalone code analysis
+│   ├── execute-*-[timestamp].md        # Ad-hoc implementation logs
+│   └── codex-execute-*-[timestamp].md  # Multi-stage execution logs
+│
+└── WFS-[topic-slug]/
+    ├── workflow-session.json        # Session metadata and state (REQUIRED)
+    ├── [.brainstorming/]           # Optional brainstorming phase (created when needed)
+    ├── [.chat/]                    # CLI interaction sessions (created when analysis is run)
+    │   ├── chat-*.md              # Saved chat sessions
+    │   └── analysis-*.md          # Analysis results
+    ├── [.process/]                 # Planning analysis results (created by /workflow:plan)
+    │   └── ANALYSIS_RESULTS.md    # Analysis results and planning artifacts
+    ├── IMPL_PLAN.md                # Planning document (REQUIRED)
+    ├── TODO_LIST.md                # Progress tracking (REQUIRED)
+    ├── [.summaries/]               # Task completion summaries (created when tasks complete)
+    │   ├── IMPL-*-summary.md      # Main task summaries
+    │   └── IMPL-*.*-summary.md    # Subtask summaries
+    └── .task/                      # Task definitions (REQUIRED)
+        ├── IMPL-*.json             # Main task definitions
+        └── IMPL-*.*.json           # Subtask definitions (created dynamically)
 ```
 
 #### Creation Strategy
 - **Initial Setup**: Create only `workflow-session.json`, `IMPL_PLAN.md`, `TODO_LIST.md`, and `.task/` directory
 - **On-Demand Creation**: Other directories created when first needed
 - **Dynamic Files**: Subtask JSON files created during task decomposition
+- **Scratchpad Usage**: `.scratchpad/` created when CLI commands run without active session
+
+#### Scratchpad Directory (.scratchpad/)
+**Purpose**: Centralized location for non-session-specific CLI outputs
+
+**When to Use**:
+1. **No Active Session**: CLI analysis/chat commands run without an active workflow session
+2. **Unrelated Analysis**: Quick analysis not related to current active session
+3. **Exploratory Work**: Ad-hoc investigation before creating formal workflow
+4. **One-Off Queries**: Standalone questions or debugging without workflow context
+
+**Output Routing Logic**:
+- **IF** active session exists AND command is session-relevant:
+  - Save to `.workflow/WFS-[id]/.chat/[command]-[timestamp].md`
+- **ELSE** (no session OR one-off analysis):
+  - Save to `.workflow/.scratchpad/[command]-[description]-[timestamp].md`
+
+**File Naming Pattern**: `[command-type]-[brief-description]-[timestamp].md`
+
+**Examples**:
+
+*Analysis Commands (read-only):*
+- `/cli:analyze "security"` (no session) → `.scratchpad/analyze-security-20250105-143022.md`
+- `/cli:chat "build process"` (unrelated to active session) → `.scratchpad/chat-build-process-20250105-143045.md`
+- `/cli:mode:plan "feature idea"` (exploratory) → `.scratchpad/plan-feature-idea-20250105-143110.md`
+- `/cli:mode:code-analysis "trace auth flow"` (no session) → `.scratchpad/code-analysis-auth-flow-20250105-143130.md`
+
+*Implementation Commands (⚠️ modifies code):*
+- `/cli:execute "implement JWT auth"` (no session) → `.scratchpad/execute-jwt-auth-20250105-143200.md`
+- `/cli:codex-execute "refactor API layer"` (no session) → `.scratchpad/codex-execute-api-refactor-20250105-143230.md`
+
+**Maintenance**:
+- Periodically review and clean up old scratchpad files
+- Promote useful analyses to formal workflow sessions if needed
+- No automatic cleanup - manual management recommended
 
 ### File Naming Conventions