docs: clarify CLI command intent and add output routing

- **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/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