feat: migrate to Gemini CLI v0.11.0-nightly with native prompt support

## Major Changes

### Gemini CLI Integration (google-gemini/gemini-cli#11228)
- Migrate from wrapper scripts to native Gemini CLI v0.11.0-nightly
- Remove `-p` flag requirement for prompt strings
- Deprecate `gemini-wrapper` and `qwen-wrapper` scripts
- Update all commands and workflows to use direct CLI syntax

### Command Syntax Updates
- **Before**: `gemini -p "CONTEXT: @**/* prompt"`
- **After**: `gemini "CONTEXT: @**/* prompt"`
- Apply to all 70+ command files and workflow templates
- Maintain backward compatibility for Qwen fallback

### File Pattern Migration
- Replace `@{CLAUDE.md}` with `@CLAUDE.md`
- Replace `@{**/*}` with `@**/*`
- Update all file references to use direct @ notation
- Remove legacy brace syntax across all documentation

### Documentation Improvements
- Reorganize `intelligent-tools-strategy.md` structure
- Add Quick Start section with decision matrix
- Enhance `--include-directories` best practices
- Add comprehensive command templates and examples
- Improve navigation with clearer section hierarchy

### Files Modified (75+ files)
- Commands: All CLI commands updated (cli/, workflow/, task/, memory/)
- Workflows: Core strategy files and templates
- Agents: CLI execution agent and doc generator
- Templates: Planning roles and tech stack guides

## Breaking Changes
- Gemini CLI v0.11.0-nightly or later required
- Old wrapper scripts no longer supported
- Legacy `@{pattern}` syntax deprecated

## Migration Guide
Users should:
1. Update Gemini CLI to v0.11.0-nightly or later
2. Remove `-p` flag from existing commands
3. Update file patterns from `@{pattern}` to `@pattern`

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

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

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

@@ -174,7 +174,7 @@ score = 0
 
 **2. Context Assembly**:
 ```bash
-CONTEXT: @{CLAUDE.md} @{discovered_file1} @{discovered_file2} ...
+CONTEXT: @CLAUDE.md @{discovered_file1} @{discovered_file2} ...
 
 ## Discovered Context
 - **Project Structure**: {module_summary}

.claude/agents/doc-generator.md

@@ -53,8 +53,7 @@ You are an expert technical documentation specialist. Your responsibility is to
 {
   "step": "analyze_module_structure",
   "action": "Deep analysis of module structure and API",
-  "command": "bash(cd src/auth && ~/.claude/scripts/gemini-wrapper -p \"PURPOSE: Document module comprehensively\nTASK: Extract module purpose, architecture, public API, dependencies\nMODE: analysis\nCONTEXT: @{**/*}
+  "command": "bash(cd src/auth && gemini \"PURPOSE: Document module comprehensively\nTASK: Extract module purpose, architecture, public API, dependencies\nMODE: analysis\nCONTEXT: @**/* System: [system_context]\nEXPECTED: Complete module analysis for documentation\nRULES: $(cat ~/.claude/workflows/cli-templates/prompts/documentation/module-documentation.txt)\")",
-         System: [system_context]\nEXPECTED: Complete module analysis for documentation\nRULES: $(cat ~/.claude/workflows/cli-templates/prompts/documentation/module-documentation.txt)\")",
   "output_to": "module_analysis",
   "on_error": "fail"
 }

.claude/commands/cli/analyze.md

@@ -67,24 +67,24 @@ The agent handles all phases internally (understanding, discovery, enhancement,
 
 ## File Pattern Auto-Detection
 
-Keywords trigger specific file patterns:
+Keywords trigger specific file patterns (each @ references one pattern):
-- "auth" → `@{**/*auth*,**/*user*}`
+- "auth" → `@**/*auth* @**/*user*`
-- "component" → `@{src/components/**/*,**/*.component.*}`
+- "component" → `@src/components/**/* @**/*.component.*`
-- "API" → `@{**/api/**/*,**/routes/**/*}`
+- "API" → `@**/api/**/* @**/routes/**/*`
-- "test" → `@{**/*.test.*,**/*.spec.*}`
+- "test" → `@**/*.test.* @**/*.spec.*`
-- "config" → `@{*.config.*,**/config/**/*}`
+- "config" → `@*.config.* @**/config/**/*`
-- Generic → `@{src/**/*}`
+- Generic → `@src/**/*`
 
 For complex patterns, use `rg` or MCP tools to discover files first, then execute CLI with precise file references.
 
 ## Command Template
 
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper -p "
+cd . && gemini -p "
 PURPOSE: [analysis goal from target]
 TASK: [auto-detected analysis type]
 MODE: analysis
-CONTEXT: @{CLAUDE.md} [auto-detected file patterns]
+CONTEXT: @CLAUDE.md [auto-detected file patterns]
 EXPECTED: Insights, patterns, recommendations (NO code modification)
 RULES: [auto-selected template] | Focus on [analysis aspect]
 "
@@ -112,7 +112,7 @@ RULES: [auto-selected template] | Focus on [analysis aspect]
 
 **Architecture Analysis**:
 ```bash
-/cli:analyze --tool qwen "component architecture"
+/cli:analyze --tool qwen -p "component architecture"
 # Executes: Qwen with component file patterns
 # Returns: Architecture review, design patterns, improvement suggestions
 ```

.claude/commands/cli/chat.md

@@ -27,7 +27,6 @@ Direct Q&A interaction with CLI tools for codebase analysis. **Analysis only - d
 - `--agent` - Use cli-execution-agent for automated context discovery (5-phase intelligent mode)
 - `--tool <codex|gemini|qwen>` - Select CLI tool (default: gemini, ignored in agent mode)
 - `--enhance` - Enhance inquiry with `/enhance-prompt` first
-- `--all-files` - Include entire codebase in context
 - `--save-session` - Save interaction to workflow session
 
 ## Execution Flow
@@ -36,7 +35,7 @@ Direct Q&A interaction with CLI tools for codebase analysis. **Analysis only - d
 
 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`
+3. Assemble context: `@CLAUDE.md` + user-specified files or `@**/*` for entire codebase
 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
@@ -54,7 +53,6 @@ Task(
     Task: ${inquiry}
     Mode: analyze (Q&A)
     Tool Preference: ${tool_flag || 'auto-select'}
-    ${all_files_flag ? 'Scope: all-files' : ''}
 
     Agent will autonomously:
     - Discover files relevant to the question
@@ -69,20 +67,20 @@ The agent handles all phases internally.
 
 ## Context Assembly
 
-**Always included**: `@{CLAUDE.md,**/*CLAUDE.md}` (project guidelines)
+**Always included**: `@CLAUDE.md @**/*CLAUDE.md` (project guidelines)
 
 **Optional**:
 - User-explicit files from inquiry keywords
-- `--all-files` flag includes entire codebase (`--all-files` wrapper parameter)
+- Use `@**/*` in CONTEXT for entire codebase
 
 For targeted analysis, use `rg` or MCP tools to discover relevant files first, then build precise CONTEXT field.
 
 ## Command Template
 
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper -p "
+cd . && gemini -p "
 INQUIRY: [user question]
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [inferred or --all-files]
+CONTEXT: @CLAUDE.md,**/*CLAUDE.md [inferred files or @**/* for all files]
 MODE: analysis
 RESPONSE: Direct answer, explanation, insights (NO code modification)
 "
@@ -110,7 +108,7 @@ RESPONSE: Direct answer, explanation, insights (NO code modification)
 
 **Architecture Question**:
 ```bash
-/cli:chat --tool qwen "how does React component optimization work here"
+/cli:chat --tool qwen -p "how does React component optimization work here"
 # Executes: Qwen architecture analysis
 # Returns: Component structure explanation, optimization patterns used
 ```
@@ -130,13 +128,6 @@ RESPONSE: Direct answer, explanation, insights (NO code modification)
 # 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**:

.claude/commands/cli/codex-execute.md

@@ -130,7 +130,7 @@ git status --short
 codex -C [dir] --full-auto exec "
 PURPOSE: [group goal]
 TASK: [subtask description - first in group]
-CONTEXT: @{relevant_files} @{CLAUDE.md}
+CONTEXT: @{relevant_files} @CLAUDE.md
 EXPECTED: [specific deliverables]
 RULES: [constraints]
 Group [X]: [group name] - Subtask 1 of N in this group
@@ -164,7 +164,7 @@ git add -A
 codex -C [dir] --full-auto exec "
 PURPOSE: [new group goal]
 TASK: [subtask description - first in new group]
-CONTEXT: @{different_files} @{CLAUDE.md}
+CONTEXT: @{different_files} @CLAUDE.md
 EXPECTED: [specific deliverables]
 RULES: [constraints]
 Group [Y]: [new group name] - Subtask 1 of N in this group

.claude/commands/cli/discuss-plan.md

@@ -69,11 +69,11 @@ Gemini analyzes the topic and proposes preliminary plan.
 ```bash
 # Round 1: CONTEXT_INPUT is the initial topic
 # Subsequent rounds: CONTEXT_INPUT is the synthesis from previous round
-~/.claude/scripts/gemini-wrapper -p "
+gemini -p "
 PURPOSE: Analyze and propose a plan for '[topic]'
 TASK: Provide initial analysis, identify key modules, and draft implementation plan
 MODE: analysis
-CONTEXT: @{CLAUDE.md} [auto-detected files]
+CONTEXT: @CLAUDE.md [auto-detected files]
 INPUT: [CONTEXT_INPUT]
 EXPECTED: Structured analysis and draft plan for discussion
 RULES: Focus on technical depth and practical considerations
@@ -90,7 +90,7 @@ codex --full-auto exec "
 PURPOSE: Critically review technical plan
 TASK: Review the provided plan, identify weaknesses, suggest alternatives, reason about trade-offs
 MODE: analysis
-CONTEXT: @{CLAUDE.md} [relevant files]
+CONTEXT: @CLAUDE.md [relevant files]
 INPUT_PLAN: [Output from Gemini's analysis]
 EXPECTED: Critical review with alternative ideas and risk analysis
 RULES: Focus on architectural soundness and implementation feasibility

.claude/commands/cli/execute.md

@@ -45,11 +45,11 @@ Auto-approves: file pattern inference, execution, **file modifications**, summar
 
 ### Context Inference
 
-Auto-selects files based on keywords and technology:
+Auto-selects files based on keywords and technology (each @ references one pattern):
-- "auth" → `@{**/*auth*,**/*user*}`
+- "auth" → `@**/*auth* @**/*user*`
-- "React" → `@{src/**/*.{jsx,tsx}}`
+- "React" → `@src/**/*.jsx @src/**/*.tsx`
-- "api" → `@{**/api/**/*,**/routes/**/*}`
+- "api" → `@**/api/**/* @**/routes/**/*`
-- Always includes: `@{CLAUDE.md,**/*CLAUDE.md}`
+- Always includes: `@CLAUDE.md @**/*CLAUDE.md`
 
 For precise file targeting, use `rg` or MCP tools to discover files first.
 
@@ -111,11 +111,11 @@ Use `resume --last` when current task extends/relates to previous execution. See
 ### Standard Mode (Default)
 ```bash
 # Gemini/Qwen: MODE=write with --approval-mode yolo
-cd . && ~/.claude/scripts/gemini-wrapper --approval-mode yolo -p "
+cd . && gemini --approval-mode yolo "
 PURPOSE: [implementation goal]
 TASK: [specific implementation]
 MODE: write
-CONTEXT: @{CLAUDE.md} [auto-detected files]
+CONTEXT: @CLAUDE.md [auto-detected files]
 EXPECTED: Working implementation with code changes
 RULES: [constraints] | Auto-approve all changes
 "

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

@@ -79,11 +79,11 @@ The agent handles all phases internally.
 ## Command Template
 
 ```bash
-cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd [directory] && gemini -p "
 PURPOSE: [bug analysis goal]
 TASK: Systematic bug analysis and fix recommendations
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+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]
 "
@@ -111,11 +111,11 @@ RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: [description]
 
 **Standard Template Example**:
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd . && gemini -p "
 PURPOSE: Debug authentication null pointer error
 TASK: Identify root cause and provide fix recommendations
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+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
 "
@@ -123,11 +123,11 @@ RULES: $(cat ~/.claude/prompt-templates/bug-fix.md) | Bug: null pointer in login
 
 **Directory-Specific**:
 ```bash
-cd src/auth && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd src/auth && gemini -p "
 PURPOSE: Fix token validation failure
 TASK: Analyze token validation bug in auth module
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+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
 "
@@ -161,4 +161,4 @@ mcp__code-index__search_code_advanced(pattern="error|exception", file_pattern="*
 - 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
+- Uses `@**/*` for in CONTEXT field for comprehensive codebase context

.claude/commands/cli/mode/code-analysis.md

@@ -82,11 +82,11 @@ The agent handles all phases internally.
 ## Command Template
 
 ```bash
-cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd [directory] && gemini -p "
 PURPOSE: [analysis goal]
 TASK: Systematic code analysis and execution path tracing
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+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]
 "
@@ -114,11 +114,11 @@ RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on [aspect]
 
 **Standard Template Example**:
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd . && gemini -p "
 PURPOSE: Trace authentication execution flow
 TASK: Analyze complete auth flow from request to response
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+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
 "
@@ -126,11 +126,11 @@ RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on control flo
 
 **Directory-Specific Analysis**:
 ```bash
-cd src/auth && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd src/auth && gemini -p "
 PURPOSE: Understand JWT token validation logic
 TASK: Trace JWT validation from middleware to service layer
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Validation flow diagram, token lifecycle analysis
 RULES: $(cat ~/.claude/prompt-templates/code-analysis.md) | Focus on security
 "
@@ -167,4 +167,4 @@ mcp__code-index__search_code_advanced(pattern="authenticate|login", file_pattern
 - 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
+- Uses `@**/*` for in CONTEXT field for comprehensive code context

.claude/commands/cli/mode/plan.md

@@ -80,11 +80,11 @@ The agent handles all phases internally.
 ## Command Template
 
 ```bash
-cd [directory] && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd [directory] && gemini -p "
 PURPOSE: [planning goal from topic]
 TASK: Comprehensive planning and architecture analysis
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md} [entire codebase in directory]
+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]
 "
@@ -112,11 +112,11 @@ RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on [topic area]
 
 **Standard Template Example**:
 ```bash
-cd . && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd . && gemini -p "
 PURPOSE: Design user dashboard architecture
 TASK: Plan dashboard component structure and data flow
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Architecture recommendations, component design, data flow diagram
 RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on scalability
 "
@@ -124,11 +124,11 @@ RULES: $(cat ~/.claude/prompt-templates/plan.md) | Focus on scalability
 
 **Directory-Specific Planning**:
 ```bash
-cd src/api && ~/.claude/scripts/gemini-wrapper --all-files -p "
+cd src/api && gemini -p "
 PURPOSE: Plan API refactoring strategy
 TASK: Analyze current API structure and recommend improvements
 MODE: analysis
-CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}
+CONTEXT: @CLAUDE.md @**/*CLAUDE.md
 EXPECTED: Refactoring roadmap, breaking change analysis, migration plan
 RULES: $(cat ~/.claude/prompt-templates/plan.md) | Maintain backward compatibility
 "
@@ -165,4 +165,4 @@ rg "architecture|design" --files-with-matches
 - 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
+- Uses `@**/*` for in CONTEXT field for comprehensive project context

.claude/commands/memory/docs.md

@@ -394,7 +394,7 @@ bash(
       },
       {
         "step": "analyze_module_tree",
-        "command": "bash(cd src/modules && ~/.claude/scripts/gemini-wrapper -p \"PURPOSE: Analyze module structure\\nTASK: Generate documentation outline\\nMODE: analysis\\nCONTEXT: @{**/*} [target_folders]\\nEXPECTED: Structure outline\\nRULES: Analyze only\")",
+        "command": "bash(cd src/modules && gemini \"PURPOSE: Analyze module structure\\nTASK: Generate documentation outline\\nMODE: analysis\\nCONTEXT: @**/* [target_folders]\\nEXPECTED: Structure outline\\nRULES: Analyze only\")",
         "output_to": "tree_outline",
         "note": "CLI for analysis only"
       }
@@ -490,7 +490,7 @@ bash(
           "CLI writes documentation to .workflow/docs/src/modules/",
           "Maintains directory structure mirroring"
         ],
-        "command": "bash(cd src/modules && ~/.claude/scripts/gemini-wrapper --approval-mode yolo -p \"PURPOSE: Generate module docs\\nTASK: Create documentation files in .workflow/docs/src/modules/\\nMODE: write\\nCONTEXT: @{**/*} [target_folders] [existing_module_docs]\\nEXPECTED: API.md and README.md in .workflow/docs/src/modules/\\nRULES: Mirror source structure, generate complete docs\")",
+        "command": "bash(cd src/modules && gemini --approval-mode yolo \"PURPOSE: Generate module docs\\nTASK: Create documentation files in .workflow/docs/src/modules/\\nMODE: write\\nCONTEXT: @**/* [target_folders] [existing_module_docs]\\nEXPECTED: API.md and README.md in .workflow/docs/src/modules/\\nRULES: Mirror source structure, generate complete docs\")",
         "depends_on": [1],
         "output": "generated_docs"
       }
@@ -533,7 +533,7 @@ bash(
       },
       {
         "step": "analyze_project",
-        "command": "bash(~/.claude/scripts/gemini-wrapper -p \"PURPOSE: Analyze project structure\\nTASK: Extract overview from modules\\nMODE: analysis\\nCONTEXT: [all_module_docs]\\nEXPECTED: Project outline\")",
+        "command": "bash(gemini \"PURPOSE: Analyze project structure\\nTASK: Extract overview from modules\\nMODE: analysis\\nCONTEXT: [all_module_docs]\\nEXPECTED: Project outline\")",
         "output_to": "project_outline"
       }
     ],
@@ -583,7 +583,7 @@ bash(
       },
       {
         "step": "analyze_architecture_and_examples",
-        "command": "bash(~/.claude/scripts/gemini-wrapper -p \"PURPOSE: Analyze system architecture and generate examples\\nTASK: Synthesize architectural overview and usage patterns\\nMODE: analysis\\nCONTEXT: [all_docs]\\nEXPECTED: Architecture outline + Examples outline\")",
+        "command": "bash(gemini \"PURPOSE: Analyze system architecture and generate examples\\nTASK: Synthesize architectural overview and usage patterns\\nMODE: analysis\\nCONTEXT: [all_docs]\\nEXPECTED: Architecture outline + Examples outline\")",
         "output_to": "arch_examples_outline"
       }
     ],
@@ -645,7 +645,7 @@ bash(
       },
       {
         "step": "analyze_api",
-        "command": "bash(~/.claude/scripts/gemini-wrapper -p \"PURPOSE: Document HTTP API\\nTASK: Analyze API endpoints\\nMODE: analysis\\nCONTEXT: @{src/api/**/*} [endpoint_discovery]\\nEXPECTED: API outline\")",
+        "command": "bash(gemini \"PURPOSE: Document HTTP API\\nTASK: Analyze API endpoints\\nMODE: analysis\\nCONTEXT: @src/api/**/* [endpoint_discovery]\\nEXPECTED: API outline\")",
         "output_to": "api_outline"
       }
     ],

.claude/commands/memory/load.md

@@ -5,7 +5,7 @@ argument-hint: "[--tool gemini|qwen] \"task context description\""
 allowed-tools: Task(*), Bash(*)
 examples:
   - /memory:load "在当前前端基础上开发用户认证功能"
-  - /memory:load --tool qwen "重构支付模块API"
+  - /memory:load --tool qwen -p "重构支付模块API"
 ---
 
 # Memory Load Command (/memory:load)
@@ -140,7 +140,7 @@ cd . && ~/.claude/scripts/${tool}-wrapper -p "
 PURPOSE: Extract project core context for task: ${task_description}
 TASK: Analyze project architecture, tech stack, key patterns, relevant files
 MODE: analysis
-CONTEXT: @{CLAUDE.md,README.md,${discovered_files}}
+CONTEXT: @CLAUDE.md,README.md @${discovered_files}
 EXPECTED: Structured project summary and integration point analysis
 RULES:
 - Focus on task-relevant core information
@@ -212,7 +212,7 @@ Before returning:
 ### Example 2: Using Qwen Tool
 
 ```bash
-/memory:load --tool qwen "重构支付模块API"
+/memory:load --tool qwen -p "重构支付模块API"
 ```
 
 Agent uses Qwen CLI for analysis, returns same structured package.

.claude/commands/workflow/review.md

@@ -99,10 +99,10 @@ After bash validation, the model takes control to:
      ```
    - Use Gemini for security analysis:
      ```bash
-     cd .workflow/${sessionId} && ~/.claude/scripts/gemini-wrapper -p "
+     cd .workflow/${sessionId} && gemini -p "
      PURPOSE: Security audit of completed implementation
      TASK: Review code for security vulnerabilities, insecure patterns, auth/authz issues
-     CONTEXT: @{.summaries/IMPL-*.md,../..,../../CLAUDE.md}
+     CONTEXT: @.summaries/IMPL-*.md,../.. @../../CLAUDE.md
      EXPECTED: Security findings report with severity levels
      RULES: Focus on OWASP Top 10, authentication, authorization, data validation, injection risks
      " --approval-mode yolo
@@ -111,10 +111,10 @@ After bash validation, the model takes control to:
    **Architecture Review** (`--type=architecture`):
    - Use Qwen for architecture analysis:
      ```bash
-     cd .workflow/${sessionId} && ~/.claude/scripts/qwen-wrapper -p "
+     cd .workflow/${sessionId} && qwen -p "
      PURPOSE: Architecture compliance review
      TASK: Evaluate adherence to architectural patterns, identify technical debt, review design decisions
-     CONTEXT: @{.summaries/IMPL-*.md,../..,../../CLAUDE.md}
+     CONTEXT: @.summaries/IMPL-*.md,../.. @../../CLAUDE.md
      EXPECTED: Architecture assessment with recommendations
      RULES: Check for patterns, separation of concerns, modularity, scalability
      " --approval-mode yolo
@@ -123,10 +123,10 @@ After bash validation, the model takes control to:
    **Quality Review** (`--type=quality`):
    - Use Gemini for code quality:
      ```bash
-     cd .workflow/${sessionId} && ~/.claude/scripts/gemini-wrapper -p "
+     cd .workflow/${sessionId} && gemini -p "
      PURPOSE: Code quality and best practices review
      TASK: Assess code readability, maintainability, adherence to best practices
-     CONTEXT: @{.summaries/IMPL-*.md,../..,../../CLAUDE.md}
+     CONTEXT: @.summaries/IMPL-*.md,../.. @../../CLAUDE.md
      EXPECTED: Quality assessment with improvement suggestions
      RULES: Check for code smells, duplication, complexity, naming conventions
      " --approval-mode yolo
@@ -143,10 +143,10 @@ After bash validation, the model takes control to:
      ' {} \;
 
      # Check implementation summaries against requirements
-     cd .workflow/${sessionId} && ~/.claude/scripts/gemini-wrapper -p "
+     cd .workflow/${sessionId} && gemini -p "
      PURPOSE: Verify all requirements and acceptance criteria are met
      TASK: Cross-check implementation summaries against original requirements
-     CONTEXT: @{.task/IMPL-*.json,.summaries/IMPL-*.md,../..,../../CLAUDE.md}
+     CONTEXT: @.task/IMPL-*.json,.summaries/IMPL-*.md,../.. @../../CLAUDE.md
      EXPECTED:
      - Requirements coverage matrix
      - Acceptance criteria verification

.claude/commands/workflow/tdd-verify.md

@@ -3,7 +3,7 @@ name: tdd-verify
 description: Verify TDD workflow compliance and generate quality report
 
 argument-hint: "[optional: WFS-session-id]"
-allowed-tools: SlashCommand(*), TodoWrite(*), Read(*), Bash(gemini-wrapper:*)
+allowed-tools: SlashCommand(*), TodoWrite(*), Read(*), Bash(gemini:*)
 ---
 
 # TDD Verification Command (/workflow:tdd-verify)
@@ -94,7 +94,7 @@ find .workflow/{sessionId}/.task/ -name '*.json' -exec jq -r '.meta.agent' {} \;
 **Gemini analysis for comprehensive TDD compliance report**
 
 ```bash
-cd project-root && ~/.claude/scripts/gemini-wrapper -p "
+cd project-root && gemini -p "
 PURPOSE: Generate TDD compliance report
 TASK: Analyze TDD workflow execution and generate quality report
 CONTEXT: @{.workflow/{sessionId}/.task/*.json,.workflow/{sessionId}/.summaries/*,.workflow/{sessionId}/.process/tdd-cycle-report.md}

.claude/commands/workflow/test-cycle-execute.md

@@ -226,11 +226,11 @@ Iteration N (managed by test-cycle-execute orchestrator):
 
 #### CLI Analysis Command (executed by orchestrator)
 ```bash
-cd {project_root} && ~/.claude/scripts/gemini-wrapper -p "
+cd {project_root} && gemini -p "
 PURPOSE: Analyze test failures and generate fix strategy
 TASK: Review test failures and identify root causes
 MODE: analysis
-CONTEXT: @{test files, implementation files}
+CONTEXT: @test files @ implementation files
 
 [Test failure context and requirements...]
 

.claude/commands/workflow/tools/task-generate-tdd.md

@@ -2,7 +2,7 @@
 name: task-generate-tdd
 description: Generate TDD task chains with Red-Green-Refactor dependencies
 argument-hint: "--session WFS-session-id [--agent]"
-allowed-tools: Read(*), Write(*), Bash(gemini-wrapper:*), TodoWrite(*)
+allowed-tools: Read(*), Write(*), Bash(gemini:*), TodoWrite(*)
 ---
 
 # TDD Task Generation Command

.claude/commands/workflow/tools/task-generate.md

@@ -256,7 +256,7 @@ This enhanced 5-field schema embeds all necessary context, artifacts, and execut
         "action": "Analyze existing code patterns and identify modification targets",
         "commands": [
           "bash(cd \"[focus_paths]\")",
-          "bash(~/.claude/scripts/gemini-wrapper -p \"PURPOSE: Identify modification targets TASK: Analyze '[title]' and locate specific files/functions/lines to modify CONTEXT: [synthesis_specification] [individual_artifacts] EXPECTED: Code locations in format 'file:function:lines' RULES: Prioritize synthesis-specification.md, identify exact modification points\")"
+          "bash(gemini \"PURPOSE: Identify modification targets TASK: Analyze '[title]' and locate specific files/functions/lines to modify CONTEXT: [synthesis_specification] [individual_artifacts] EXPECTED: Code locations in format 'file:function:lines' RULES: Prioritize synthesis-specification.md, identify exact modification points\")"
         ],
         "output_to": "task_context_with_targets",
         "on_error": "fail"

.claude/commands/workflow/tools/test-concept-enhanced.md

@@ -48,7 +48,7 @@ Specialized analysis tool for test generation workflows that uses Gemini to anal
 
 **Tool Configuration**:
 ```bash
-cd .workflow/{test_session_id}/.process && ~/.claude/scripts/gemini-wrapper -p "
+cd .workflow/{test_session_id}/.process && gemini -p "
 PURPOSE: Analyze test coverage gaps and design comprehensive test generation strategy
 TASK: Study implementation context, existing tests, and generate test requirements for missing coverage
 MODE: analysis

.claude/commands/workflow/tools/test-task-generate.md

@@ -198,7 +198,7 @@ Generate **TWO task JSON files**:
         "Codex generates comprehensive test suite",
         "Codex validates test syntax and executability"
       ],
-      "command": "bash(codex -C [focus_paths] --full-auto exec \"PURPOSE: Generate comprehensive test suite TASK: Create test files based on TEST_ANALYSIS_RESULTS.md section 5 MODE: write CONTEXT: @{.workflow/WFS-test-[session]/.process/TEST_ANALYSIS_RESULTS.md,.workflow/WFS-test-[session]/.process/test-context-package.json} EXPECTED: All test files with happy path, error handling, edge cases, integration tests RULES: Follow test framework conventions, ensure tests are executable\" --skip-git-repo-check -s danger-full-access)",
+      "command": "bash(codex -C [focus_paths] --full-auto exec \"PURPOSE: Generate comprehensive test suite TASK: Create test files based on TEST_ANALYSIS_RESULTS.md section 5 MODE: write CONTEXT: @.workflow/WFS-test-[session]/.process/TEST_ANALYSIS_RESULTS.md @.workflow/WFS-test-[session]/.process/test-context-package.json EXPECTED: All test files with happy path, error handling, edge cases, integration tests RULES: Follow test framework conventions, ensure tests are executable\" --skip-git-repo-check -s danger-full-access)",
       "depends_on": [],
       "output": "test_generation"
     }],
@@ -323,7 +323,7 @@ Generate **TWO task JSON files**:
           "cycle_pattern": "test → gemini_diagnose → manual_fix (or codex if needed) → retest",
           "tools": {
             "test_execution": "bash(test_command)",
-            "diagnosis": "gemini-wrapper (MODE: analysis, uses bug-fix template)",
+            "diagnosis": "gemini (MODE: analysis, uses bug-fix template)",
             "fix_application": "manual (default) or codex exec resume --last (if explicitly needed)",
             "verification": "bash(test_command) + regression_check"
           },
@@ -354,11 +354,11 @@ Generate **TWO task JSON files**:
         "      * Source files from focus_paths",
         "      * Implementation summaries from source session",
         "    - Execute Gemini analysis with bug-fix template:",
-        "      bash(cd .workflow/WFS-test-[session]/.process && ~/.claude/scripts/gemini-wrapper --all-files -p \"",
+        "      bash(cd .workflow/WFS-test-[session]/.process && gemini \"",
         "      PURPOSE: Diagnose test failure iteration [N] and propose minimal fix",
         "      TASK: Systematic bug analysis and fix recommendations for test failure",
         "      MODE: analysis",
-        "      CONTEXT: @{CLAUDE.md,**/*CLAUDE.md}",
+        "      CONTEXT: @CLAUDE.md,**/*CLAUDE.md",
         "               Test output: [test_failures]",
         "               Source files: [focus_paths]",
         "               Implementation: [implementation_context]",

.claude/scripts/update_module_claude.sh

@@ -88,8 +88,7 @@ update_module_claude() {
     
     # Use unified template for all modules
     local template_path="$HOME/.claude/workflows/cli-templates/prompts/memory/claude-module-unified.txt"
-    local analysis_strategy="--all-files"
+
-    
     # Prepare logging info
     local module_name=$(basename "$module_path")
 
@@ -131,8 +130,10 @@ update_module_claude() {
 
     $template_content
 
-    $update_context"
+    $update_context
-    
+
+    CONTEXT: @**/*"
+
     # Execute update
     local start_time=$(date +%s)
     echo "   🔄 Starting update..."
@@ -146,10 +147,11 @@ update_module_claude() {
         - Path: $module_path
         - Tool: $tool"
 
-        # Execute with selected tool (always use --all-files)
+        # Execute with selected tool
+        # NOTE: Prompt is passed via -p flag for gemini/qwen, first parameter for codex
         case "$tool" in
             qwen)
-                qwen --all-files --yolo -p "$final_prompt" 2>&1
+                qwen -p "$final_prompt" --yolo 2>&1
                 tool_result=$?
                 ;;
             codex)
@@ -157,7 +159,7 @@ update_module_claude() {
                 tool_result=$?
                 ;;
             gemini|*)
-                gemini --all-files --yolo -p "$final_prompt" 2>&1
+                gemini -p "$final_prompt" --yolo 2>&1
                 tool_result=$?
                 ;;
         esac

.claude/skills/prompt-enhancer/SKILL.md

@@ -1,124 +0,0 @@
----
-name: Prompt Enhancer
-description: Transform vague prompts into actionable specs using intelligent analysis and session memory. Use when user input contains -e or --enhance flag.
-allowed-tools: (none)
----
-
-# Prompt Enhancer
-
-**Transform**: Vague intent → Structured specification (Memory-based, Direct Output)
-
-**Languages**: English + Chinese (中英文语义识别)
-
-## Process (Internal → Direct Output)
-
-**Internal Analysis**: Intelligently extract session context, identify tech stack, and structure into actionable format.
-
-**Output**: Direct structured prompt (no intermediate steps shown)
-
-## Output Format
-
-**Dynamic Structure**: Adapt fields based on task type and context needs. Not all fields are required.
-
-**Core Fields** (always present):
-- **INTENT**: One-sentence technical goal
-- **ACTION**: Concrete steps with technical details
-
-**Optional Fields** (include when relevant):
-- **TECH STACK**: Relevant technologies (when tech-specific)
-- **CONTEXT**: Session memory findings (when context matters)
-- **ATTENTION**: Critical constraints (when risks/requirements exist)
-- **SCOPE**: Affected modules/files (for multi-module tasks)
-- **METRICS**: Success criteria (for optimization/performance tasks)
-- **DEPENDENCIES**: Related components (for integration tasks)
-
-**Example (Simple Task)**:
-```
-📋 ENHANCED PROMPT
-
-INTENT: Fix authentication token validation in JWT middleware
-
-ACTION:
-1. Review token expiration logic in auth middleware
-2. Add proper error handling for expired tokens
-3. Test with valid/expired/malformed tokens
-```
-
-**Example (Complex Task)**:
-```
-📋 ENHANCED PROMPT
-
-INTENT: Optimize API performance with caching and database indexing
-
-TECH STACK:
-- Redis: Response caching
-- PostgreSQL: Query optimization
-
-CONTEXT:
-- API response times >2s mentioned in previous conversation
-- PostgreSQL slow query logs show N+1 problems
-
-ACTION:
-1. Profile endpoints to identify slow queries
-2. Add PostgreSQL indexes on frequently queried columns
-3. Implement Redis caching for read-heavy endpoints
-4. Add cache invalidation on data updates
-
-METRICS:
-- Target: <500ms API response time
-- Cache hit ratio: >80%
-
-ATTENTION:
-- Maintain backward compatibility with existing API contracts
-- Handle cache invalidation correctly to avoid stale data
-```
-## Workflow
-
-```
-Trigger (-e/--enhance) → Internal Analysis → Dynamic Output
-         ↓                       ↓                  ↓
-   User Input           Assess Task Type      Select Fields
-                    Extract Memory Context    Structure Prompt
-```
-
-1. **Detect**: User input contains `-e` or `--enhance`
-2. **Analyze**:
-   - Determine task type (fix/optimize/implement/refactor)
-   - Extract relevant session context
-   - Identify tech stack and constraints
-3. **Structure**:
-   - Always include: INTENT + ACTION
-   - Conditionally add: TECH STACK, CONTEXT, ATTENTION, METRICS, etc.
-4. **Output**: Present dynamically structured prompt
-
-## Enhancement Guidelines (Internal)
-
-**Always Include**:
-- Clear, actionable INTENT
-- Concrete ACTION steps with technical details
-
-**Add When Relevant**:
-- TECH STACK: Task involves specific technologies
-- CONTEXT: Session memory provides useful background
-- ATTENTION: Security/compatibility/performance concerns exist
-- SCOPE: Multi-module or cross-component changes
-- METRICS: Performance/optimization goals need measurement
-- DEPENDENCIES: Integration points matter
-
-**Quality Checks**:
-- Make vague intent explicit
-- Resolve ambiguous references
-- Add testing/validation steps
-- Include constraints from memory
-
-## Best Practices
-
-- ✅ Trigger only on `-e`/`--enhance` flags
-- ✅ Use **dynamic field selection** based on task type
-- ✅ Extract **memory context ONLY** (no file reading)
-- ✅ Always include INTENT + ACTION as core fields
-- ✅ Add optional fields only when relevant to task
-- ✅ Direct output (no intermediate steps shown)
-- ❌ NO tool calls
-- ❌ NO file operations (Bash, Read, Glob, Grep)
-- ❌ NO fixed template - adapt to task needs

.claude/workflows/cli-templates/prompts/workflow/task-json-cli-mode.txt

@@ -148,10 +148,10 @@ bash(codex --full-auto exec "..." resume --last --skip-git-repo-check -s danger-
 
 ### Gemini/Qwen Commands (Analysis/Documentation)
 ```bash
-bash(~/.claude/scripts/gemini-wrapper -p "PURPOSE: {purpose} TASK: {task} MODE: analysis CONTEXT: @{{synthesis_spec_path}} EXPECTED: {expected} RULES: {rules}")
+bash(gemini "PURPOSE: {purpose} TASK: {task} MODE: analysis CONTEXT: @{synthesis_spec_path} EXPECTED: {expected} RULES: {rules}")
 
 # With write permission
-bash(~/.claude/scripts/gemini-wrapper --approval-mode yolo -p "PURPOSE: {purpose} TASK: {task} MODE: write CONTEXT: @{{context}} EXPECTED: {expected} RULES: {rules}")
+bash(gemini --approval-mode yolo "PURPOSE: {purpose} TASK: {task} MODE: write CONTEXT: @{context} EXPECTED: {expected} RULES: {rules}")
 ```
 
 ## Field Descriptions
@@ -175,4 +175,4 @@ bash(~/.claude/scripts/gemini-wrapper --approval-mode yolo -p "PURPOSE: {purpose
 5. **Step Dependencies**: Use `depends_on: [1, 2]` to specify execution order
 6. **Parameter Position**:
    - Codex: `--skip-git-repo-check -s danger-full-access` at END
-   - Gemini/Qwen: `--approval-mode yolo` AFTER wrapper command, BEFORE -p
+   - Gemini/Qwen: `--approval-mode yolo` BEFORE the prompt

.claude/workflows/context-search-strategy.md

@@ -40,8 +40,8 @@ type: search-guideline
 ### Quick Command Reference
 ```bash
 # Semantic File Discovery (codebase-retrieval)
-~/.claude/scripts/gemini-wrapper --all-files -p "List all files relevant to: [task/feature description]"
+gemini "CONTEXT: @**/* List all files relevant to: [task/feature description]"
-bash(~/.claude/scripts/gemini-wrapper --all-files -p "List all files relevant to: [task/feature description]")
+bash(gemini "CONTEXT: @**/* List all files relevant to: [task/feature description]")
 
 # Program Architecture Analysis (MANDATORY FIRST)
 ~/.claude/scripts/get_modules_by_depth.sh  # Discover program architecture
@@ -65,7 +65,7 @@ grep -n -i "pattern" file.txt   # Line numbers, case-insensitive
 ### Workflow Integration Examples
 ```bash
 # Semantic Discovery → Content Search → Analysis (Recommended Pattern)
-~/.claude/scripts/gemini-wrapper --all-files -p "List all files relevant to: [task/feature]"  # Get relevant files
+gemini "CONTEXT: @**/* List all files relevant to: [task/feature]"  # Get relevant files
 rg "[pattern]" --type [filetype]  # Then search within discovered files
 
 # Program Architecture Analysis (MANDATORY BEFORE PLANNING)

.claude/workflows/intelligent-tools-strategy.md

@@ -7,67 +7,77 @@ type: strategic-guideline
 # Intelligent Tools Selection Strategy
 
 ## 📋 Table of Contents
-1. [Core Framework](#-core-framework)
+1. [Quick Start](#-quick-start)
 2. [Tool Specifications](#-tool-specifications)
 3. [Command Templates](#-command-templates)
-4. [Tool Selection Guide](#-tool-selection-guide)
+4. [Execution Configuration](#-execution-configuration)
-5. [Usage Patterns](#-usage-patterns)
+5. [Best Practices](#-best-practices)
-6. [Best Practices](#-best-practices)
 
 ---
 
-## ⚡ Core Framework
+## ⚡ Quick Start
 
 ### Tool Overview
 - **Gemini**: Analysis, understanding, exploration & documentation (primary)
 - **Qwen**: Analysis, understanding, exploration & documentation (fallback, same capabilities as Gemini)
 - **Codex**: Development, implementation & automation
 
-### Decision Principles
+### Quick Decision Matrix
+
+| Scenario | Tool | Command Pattern |
+|----------|------|-----------------|
+| **Exploring/Understanding** | Gemini → Qwen | `cd [dir] && gemini "PURPOSE:... CONTEXT: @**/*"` |
+| **Architecture/Analysis** | Gemini → Qwen | `cd [dir] && gemini "PURPOSE:... CONTEXT: @**/*"` |
+| **Building/Fixing** | Codex | `codex -C [dir] --full-auto exec "PURPOSE:... MODE: auto"` |
+| **Not sure?** | Multiple | Use tools in parallel |
+| **Small task?** | Still use tools | Tools are faster than manual work |
+
+### Core Principles
 - **Use tools early and often** - Tools are faster, more thorough, and reliable than manual approaches
 - **When in doubt, use both** - Parallel usage provides comprehensive coverage
 - **Default to tools** - Use specialized tools for most coding tasks, no matter how small
 - **Lower barriers** - Engage tools immediately when encountering any complexity
-- **Context optimization** - Based on user intent, determine whether to use `-C [directory]` parameter for focused analysis to reduce irrelevant context import
 - **⚠️ Write operation protection** - For local codebase write/modify operations, require EXPLICIT user confirmation unless user provides clear instructions containing MODE=write or MODE=auto
 
-### Quick Decision Rules
-1. **Exploring/Understanding?** → Start with Gemini (fallback to Qwen if needed)
-2. **Architecture/Analysis?** → Start with Gemini (fallback to Qwen if needed)
-3. **Building/Fixing?** → Start with Codex
-4. **Not sure?** → Use multiple tools in parallel
-5. **Small task?** → Still use tools - they're faster than manual work
-
 ---
 
 ## 🎯 Tool Specifications
 
-### Gemini
+### Gemini & Qwen
-- **Command**: `~/.claude/scripts/gemini-wrapper`
+
+#### Overview
+- **Commands**: `gemini` (primary) | `qwen` (fallback)
 - **Strengths**: Large context window, pattern recognition
-- **Best For**: Analysis, documentation generation, code exploration
+- **Best For**: Analysis, documentation generation, code exploration, architecture review
-- **Permissions**: Default read-only analysis, MODE=write requires explicit specification (auto-enables --approval-mode yolo)
+- **Permissions**: Default read-only analysis, MODE=write requires explicit specification
 - **Default MODE**: `analysis` (read-only)
 - **⚠️ Write Trigger**: Only when user explicitly requests "generate documentation", "modify code", or specifies MODE=write
+- **Priority**: Prefer Gemini; use Qwen as fallback when Gemini unavailable
 
 #### MODE Options
-- `analysis` (default) - Read-only analysis and documentation generation
-- `write` - ⚠️ Create/modify codebase files (requires explicit specification, auto-enables --approval-mode yolo)
 
-### Qwen
+**analysis** (default) - Read-only analysis and documentation generation
-- **Command**: `~/.claude/scripts/qwen-wrapper`
+- **⚠️ CRITICAL CONSTRAINT**: Absolutely NO file creation, modification, or deletion operations
-- **Strengths**: Large context window, pattern recognition (same as Gemini)
+- Analysis output should be returned as text response only
-- **Best For**: Analysis, documentation generation, code exploration (fallback option when Gemini unavailable)
+- Use for: code review, architecture analysis, pattern discovery, documentation reading
-- **Permissions**: Default read-only analysis, MODE=write requires explicit specification (auto-enables --approval-mode yolo)
-- **Default MODE**: `analysis` (read-only)
-- **⚠️ Write Trigger**: Only when user explicitly requests "generate documentation", "modify code", or specifies MODE=write
-- **Priority**: Secondary to Gemini - use as fallback for same tasks
 
-#### MODE Options
+**write** - ⚠️ Create/modify codebase files (requires explicit specification, auto-enables --approval-mode yolo)
-- `analysis` (default) - Read-only analysis and documentation generation (same as Gemini)
+- Use for: generating documentation files, creating code files, modifying existing files
-- `write` - ⚠️ Create/modify codebase files (requires explicit specification, auto-enables --approval-mode yolo)
+
+#### Tool Selection
+```bash
+# Default: Use Gemini
+gemini "analysis prompt"
+
+# Fallback: Use Qwen if Gemini unavailable
+qwen "analysis prompt"
+```
+
+---
 
 ### Codex
+
+#### Overview
 - **Command**: `codex --full-auto exec`
 - **Strengths**: Autonomous development, mathematical reasoning
 - **Best For**: Implementation, testing, automation
@@ -76,27 +86,39 @@ type: strategic-guideline
 - **⚠️ Write Trigger**: Only when user explicitly requests "implement", "modify", "generate code" AND specifies MODE
 
 #### MODE Options
-- `auto` - ⚠️ Autonomous development with full file operations (requires explicit specification, enables -s danger-full-access)
+
-- `write` - ⚠️ Test generation and file modification (requires explicit specification)
+**auto** - ⚠️ Autonomous development with full file operations
-- **Default**: No default mode, MODE must be explicitly specified
+- Requires explicit specification
+- Enables `-s danger-full-access`
+- Use for: feature implementation, bug fixes, autonomous development
+
+**write** - ⚠️ Test generation and file modification
+- Requires explicit specification
+- Use for: test generation, focused file modifications
 
 #### Session Management
-- `codex resume` - Resume previous interactive session (picker by default)
-- `codex exec "task" resume --last` - Continue most recent session with new task (maintains context)
-- `codex -i <image_file>` - Attach image(s) to initial prompt (useful for UI/design references)
-- **Multi-task Pattern**: First task uses `exec`, subsequent tasks use `exec "..." resume --last` for context continuity
-  - **Parameter Position**: `resume --last` must be placed AFTER the prompt string at command END
-  - **Example**:
-    ```bash
-    # First task - establish session
-    codex -C project --full-auto exec "Implement auth module" --skip-git-repo-check -s danger-full-access
 
-    # Subsequent tasks - continue same session
+**Basic Commands**:
-    codex --full-auto exec "Add JWT validation" resume --last --skip-git-repo-check -s danger-full-access
+- `codex resume` - Resume previous interactive session (picker by default)
-    codex --full-auto exec "Write auth tests" resume --last --skip-git-repo-check -s danger-full-access
+- `codex resume --last` - Resume most recent session directly
-    ```
+- `codex -i <image_file>` - Attach image(s) to initial prompt (useful for UI/design references)
+
+**Multi-task Pattern**: First task uses `exec`, subsequent tasks use `exec "..." resume --last` for context continuity
+
+**Parameter Position**: `resume --last` must be placed AFTER the prompt string at command END
+
+**Example**:
+```bash
+# First task - establish session
+codex -C project --full-auto exec "Implement auth module" --skip-git-repo-check -s danger-full-access
+
+# Subsequent tasks - continue same session
+codex --full-auto exec "Add JWT validation" resume --last --skip-git-repo-check -s danger-full-access
+codex --full-auto exec "Write auth tests" resume --last --skip-git-repo-check -s danger-full-access
+```
 
 #### Auto-Resume Decision Rules
+
 **When to use `resume --last`**:
 - Current task is related to/extends previous Codex task in conversation memory
 - Current task requires context from previous implementation
@@ -114,6 +136,7 @@ type: strategic-guideline
 ## 🎯 Command Templates
 
 ### Universal Template Structure
+
 Every command MUST follow this structure:
 - [ ] **PURPOSE** - Clear goal and intent
 - [ ] **TASK** - Specific execution task
@@ -122,57 +145,41 @@ Every command MUST follow this structure:
 - [ ] **EXPECTED** - Clear expected results
 - [ ] **RULES** - Template reference and constraints
 
+---
+
 ### Standard Command Formats
 
-#### Gemini Commands
+#### Gemini & Qwen Commands
+
 ```bash
-# Gemini Analysis (read-only, default)
+# Analysis Mode (read-only, default)
-cd [directory] && ~/.claude/scripts/gemini-wrapper -p "
+# Use 'gemini' (primary) or 'qwen' (fallback)
+cd [directory] && gemini "
 PURPOSE: [clear analysis goal]
 TASK: [specific analysis task]
 MODE: analysis
-CONTEXT: [file references and memory context]
+CONTEXT: @**/* [default: all files, or specify file patterns]
 EXPECTED: [expected output]
 RULES: [template reference and constraints]
 "
 
-# Gemini Write Mode (requires explicit MODE=write)
+# Write Mode (requires explicit MODE=write)
-# NOTE: --approval-mode yolo must be placed AFTER wrapper command, BEFORE -p
+# NOTE: --approval-mode yolo must be placed AFTER the prompt
-cd [directory] && ~/.claude/scripts/gemini-wrapper --approval-mode yolo -p "
+cd [directory] && gemini "
 PURPOSE: [clear goal]
 TASK: [specific task]
 MODE: write
-CONTEXT: [file references and memory context]
+CONTEXT: @**/* [default: all files, or specify file patterns]
 EXPECTED: [expected output]
 RULES: [template reference and constraints]
-"
+" --approval-mode yolo
-```
 
-#### Qwen Commands
+# Fallback: Replace 'gemini' with 'qwen' if Gemini unavailable
-```bash
+cd [directory] && qwen "..." # Same syntax as gemini
-# Qwen Analysis (read-only, default) - Same as Gemini, use as fallback
-cd [directory] && ~/.claude/scripts/qwen-wrapper -p "
-PURPOSE: [clear analysis goal]
-TASK: [specific analysis task]
-MODE: analysis
-CONTEXT: [file references and memory context]
-EXPECTED: [expected output]
-RULES: [template reference and constraints]
-"
-
-# Qwen Write Mode (requires explicit MODE=write)
-# NOTE: --approval-mode yolo must be placed AFTER wrapper command, BEFORE -p
-cd [directory] && ~/.claude/scripts/qwen-wrapper --approval-mode yolo -p "
-PURPOSE: [clear goal]
-TASK: [specific task]
-MODE: write
-CONTEXT: [file references and memory context]
-EXPECTED: [expected output]
-RULES: [template reference and constraints]
-"
 ```
 
 #### Codex Commands
+
 ```bash
 # Codex Development (requires explicit MODE=auto)
 # NOTE: --skip-git-repo-check and -s danger-full-access must be placed at command END
@@ -180,7 +187,7 @@ codex -C [directory] --full-auto exec "
 PURPOSE: [clear development goal]
 TASK: [specific development task]
 MODE: auto
-CONTEXT: [file references and memory context]
+CONTEXT: @**/* [default: all files, or specify file patterns and memory context]
 EXPECTED: [expected deliverables]
 RULES: [template reference and constraints]
 " --skip-git-repo-check -s danger-full-access
@@ -191,48 +198,79 @@ codex -C [directory] --full-auto exec "
 PURPOSE: [clear goal]
 TASK: [specific task]
 MODE: write
-CONTEXT: [file references and memory context]
+CONTEXT: @**/* [default: all files, or specify file patterns and memory context]
 EXPECTED: [expected deliverables]
 RULES: [template reference and constraints]
 " --skip-git-repo-check -s danger-full-access
 ```
 
+---
+
 ### Directory Context Configuration
-Tools execute in current working directory:
+
-- **Gemini**: `cd path/to/project && ~/.claude/scripts/gemini-wrapper -p "prompt"`
+**Tool Directory Navigation**:
-- **Qwen**: `cd path/to/project && ~/.claude/scripts/qwen-wrapper -p "prompt"`
+- **Gemini & Qwen**: `cd path/to/project && gemini "prompt"` (or `qwen`)
 - **Codex**: `codex -C path/to/project --full-auto exec "task"` (Codex still supports -C)
 - **Path types**: Supports both relative (`../project`) and absolute (`/full/path`) paths
-- **Token analysis**: For gemini-wrapper and qwen-wrapper, token counting happens in current directory
+- **Token analysis**: For Gemini/Qwen, token counting happens in current directory
 
-### RULES Field Format
+#### Multi-Directory Support (Gemini & Qwen)
+
+**Purpose**: For large projects requiring fine-grained access across multiple directories
+
+**Use Case**: When `cd` limits global visibility but you need to reference files from other folders
+
+**Parameter**: `--include-directories <dir1,dir2,...>`
+- Includes additional directories in the workspace
+- Can be specified multiple times or as comma-separated values
+- Maximum 5 directories can be added
+- Particularly useful when working in a subdirectory but needing context from parent or sibling directories
+
+**Syntax Options**:
 ```bash
-RULES: $(cat "~/.claude/workflows/cli-templates/prompts/[category]/[template].txt") | [constraints]
+# Comma-separated format
+gemini "prompt" --include-directories /path/to/project1,/path/to/project2
+
+# Multiple flags format
+gemini "prompt" --include-directories /path/to/project1 --include-directories /path/to/project2
+
+# Combined with cd for focused analysis with extended context (RECOMMENDED)
+cd src/auth && gemini "
+PURPOSE: Analyze authentication with shared utilities context
+TASK: Review auth implementation and its dependencies
+MODE: analysis
+CONTEXT: @**/* (includes current dir + shared + types directories)
+EXPECTED: Complete analysis with cross-directory dependencies
+RULES: Focus on integration patterns
+" --include-directories ../shared,../types
 ```
 
-**⚠️ CRITICAL: Command Substitution Rules**
+**Best Practices**:
-When using `$(cat ...)` for template loading in actual CLI commands:
+- **Recommended Pattern**: Use `cd` to navigate to primary focus directory, then use `--include-directories` for additional context
-- **Template reference only, never read**: When user specifies template name, use `$(cat ...)` directly in RULES field, do NOT read template content first
+  - Example: `cd src/auth && gemini "..." --include-directories ../shared,../types`
-- **NEVER use escape characters**: `\$`, `\"`, `\'` will break command substitution
+  - Benefits: More precise file references (relative to current directory), clearer intent, better context control
-- **In -p "..." context**: Path in `$(cat ...)` needs NO quotes (tilde expands correctly)
+- Use when `cd` alone limits necessary context visibility
-- **Correct**: `RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/pattern.txt)`
+- Keep directory count ≤ 5 for optimal performance
-- **WRONG**: `RULES: \$(cat ...)` or `RULES: $(cat \"...\")` or `RULES: $(cat '...')`
+- Combine with specific file patterns in CONTEXT for precision
-- **Why**: Shell executes `$(...)` in subshell where path is safe without quotes
+- Prefer `cd + --include-directories` over multiple `cd` commands for cross-directory analysis
 
-**Examples**:
+---
-- Single template: `$(cat "~/.claude/workflows/cli-templates/prompts/analysis/pattern.txt") | Focus on security`
-- Multiple templates: `$(cat "template1.txt") $(cat "template2.txt") | Enterprise standards`
-- No template: `Focus on security patterns, include dependency analysis`
-- File patterns: `@{src/**/*.ts,CLAUDE.md} - Stay within scope`
 
-### File Pattern Reference
+### CONTEXT Field Configuration
-- All files: `@{**/*}`
+
-- Source files: `@{src/**/*}`
+#### File Pattern Reference
-- TypeScript: `@{*.ts,*.tsx}`
+
-- With docs: `@{CLAUDE.md,**/*CLAUDE.md}`
+**Default Pattern**:
-- Tests: `@{src/**/*.test.*}`
+- **All files (default)**: `@**/*` - Use this as default for comprehensive context
+
+**Common Patterns**:
+- Source files: `@src/**/*`
+- TypeScript: `@*.ts @*.tsx` (multiple @ for multiple patterns)
+- With docs: `@CLAUDE.md @**/*CLAUDE.md` (multiple @ for multiple patterns)
+- Tests: `@src/**/*.test.*`
+
+#### Complex Pattern Discovery
 
-**Complex Pattern Discovery**:
 For complex file pattern requirements, use semantic discovery tools BEFORE CLI execution:
 - **rg (ripgrep)**: Content-based file discovery with regex patterns
 - **Code Index MCP**: Semantic file search based on task requirements
@@ -245,14 +283,14 @@ rg "export.*Component" --files-with-matches --type ts  # Find component files
 mcp__code-index__search_code_advanced(pattern="interface.*Props", file_pattern="*.tsx")  # Find interface files
 
 # Step 2: Build precise CONTEXT from discovery results
-CONTEXT: @{src/components/Auth.tsx,src/types/auth.d.ts,src/hooks/useAuth.ts}
+CONTEXT: @src/components/Auth.tsx @src/types/auth.d.ts @src/hooks/useAuth.ts
 
 # Step 3: Execute CLI with precise file references
-cd src && ~/.claude/scripts/gemini-wrapper -p "
+cd src && gemini "
 PURPOSE: Analyze authentication components
 TASK: Review auth component patterns and props interfaces
 MODE: analysis
-CONTEXT: @{components/Auth.tsx,types/auth.d.ts,hooks/useAuth.ts}
+CONTEXT: @components/Auth.tsx @types/auth.d.ts @hooks/useAuth.ts
 EXPECTED: Pattern analysis and improvement suggestions
 RULES: Focus on type safety and component composition
 "
@@ -260,26 +298,38 @@ RULES: Focus on type safety and component composition
 
 ---
 
-## 📊 Tool Selection Guide
+### RULES Field Configuration
 
-### Selection Matrix
+#### Basic Format
+```bash
+RULES: $(cat ~/.claude/workflows/cli-templates/prompts/[category]/[template].txt) | [constraints]
+```
 
-| Task Type | Tool | Use Case | Template |
+#### ⚠️ CRITICAL: Command Substitution Rules
-|-----------|------|----------|-----------|
+
-| **Analysis** | Gemini (Qwen fallback) | Code exploration, architecture review, patterns | `analysis/pattern.txt` |
+When using `$(cat ...)` for template loading in actual CLI commands:
-| **Architecture** | Gemini (Qwen fallback) | System design, architectural analysis | `analysis/architecture.txt` |
+- **Template reference only, never read**: When user specifies template name, use `$(cat ...)` directly in RULES field, do NOT read template content first
-| **Documentation** | Gemini (Qwen fallback) | Code docs, API specs, guides | `analysis/quality.txt` |
+- **NEVER use escape characters**: `\$`, `\"`, `\'` will break command substitution
-| **Development** | Codex | Feature implementation, bug fixes, testing | `development/feature.txt` |
+- **In prompt context**: Path in `$(cat ...)` needs NO quotes (tilde expands correctly)
-| **Planning** | Gemini/Qwen | Task breakdown, migration planning | `planning/task-breakdown.txt` |
+- **Correct**: `RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/pattern.txt)`
-| **Security** | Codex | Vulnerability assessment, fixes | `analysis/security.txt` |
+- **WRONG**: `RULES: \$(cat ...)` or `RULES: $(cat \"...\")` or `RULES: $(cat '...')`
-| **Refactoring** | Multiple | Gemini/Qwen for analysis, Codex for execution | `development/refactor.txt` |
+- **Why**: Shell executes `$(...)` in subshell where path is safe without quotes
-| **Module Documentation** | Gemini (Qwen fallback) | Universal module/file documentation for all levels | `memory/claude-module-unified.txt` |
+
+#### Examples
+- Single template: `$(cat ~/.claude/workflows/cli-templates/prompts/analysis/pattern.txt) | Focus on security`
+- Multiple templates: `$(cat template1.txt) $(cat template2.txt) | Enterprise standards`
+- No template: `Focus on security patterns, include dependency analysis`
+- File patterns: `@src/**/*.ts @CLAUDE.md - Stay within scope`
+
+---
 
 ### Template System
 
-**Base Structure**: `~/.claude/workflows/cli-templates/`
+#### Base Structure
+`~/.claude/workflows/cli-templates/`
 
 #### Available Templates
+
 ```
 prompts/
 ├── analysis/
@@ -307,11 +357,103 @@ tech-stacks/
 └── react-dev.md         - React architecture
 ```
 
+#### Task-Template Selection Matrix
+
+| Task Type | Tool | Use Case | Template |
+|-----------|------|----------|-----------|
+| **Analysis** | Gemini (Qwen fallback) | Code exploration, architecture review, patterns | `analysis/pattern.txt` |
+| **Architecture** | Gemini (Qwen fallback) | System design, architectural analysis | `analysis/architecture.txt` |
+| **Documentation** | Gemini (Qwen fallback) | Code docs, API specs, guides | `analysis/quality.txt` |
+| **Development** | Codex | Feature implementation, bug fixes, testing | `development/feature.txt` |
+| **Planning** | Gemini/Qwen | Task breakdown, migration planning | `planning/task-breakdown.txt` |
+| **Security** | Codex | Vulnerability assessment, fixes | `analysis/security.txt` |
+| **Refactoring** | Multiple | Gemini/Qwen for analysis, Codex for execution | `development/refactor.txt` |
+| **Module Documentation** | Gemini (Qwen fallback) | Universal module/file documentation for all levels | `memory/claude-module-unified.txt` |
+
 ---
 
-## 🚀 Usage Patterns
+## ⚙️ Execution Configuration
+
+### Dynamic Timeout Allocation
+
+**Timeout Ranges**:
+- **Simple tasks** (analysis, search): 20-40min (1200000-2400000ms)
+- **Medium tasks** (refactoring, documentation): 40-60min (2400000-3600000ms)
+- **Complex tasks** (implementation, migration): 60-120min (3600000-7200000ms)
+
+**Codex Multiplier**: Codex commands use 1.5x of allocated time
+
+**Application**: All bash() wrapped commands including Gemini, Qwen and Codex executions
+
+**Auto-detection**: Analyze PURPOSE and TASK fields to determine appropriate timeout
+
+**Command Examples**:
+```bash
+bash(gemini "prompt")  # Simple analysis: 20-40min
+bash(codex -C directory --full-auto exec "task")  # Complex implementation: 90-180min
+```
+
+---
+
+### Permission Framework
+
+#### Write Operation Protection
+
+**⚠️ WRITE PROTECTION**: Local codebase write/modify requires EXPLICIT user confirmation
+
+**Mode Hierarchy**:
+- **Analysis Mode (default)**: Read-only, safe for auto-execution
+- **Write Mode**: Requires user explicitly states MODE=write or MODE=auto in prompt
+- **Exception**: User provides clear instructions like "modify", "create", "implement"
+
+#### Tool-Specific Permissions
+
+**Gemini/Qwen Write Access**:
+- Use `--approval-mode yolo` ONLY when MODE=write explicitly specified
+- **Parameter Position**: Place AFTER the prompt: `gemini "..." --approval-mode yolo`
+
+**Codex Write Access**:
+- Use `-s danger-full-access` and `--skip-git-repo-check` ONLY when MODE=auto explicitly specified
+- **Parameter Position**: Place AFTER the prompt string at command END: `codex ... exec "..." --skip-git-repo-check -s danger-full-access`
+
+**Default Behavior**: All tools default to analysis/read-only mode without explicit write permission
+
+---
+
+## 🔧 Best Practices
+
+### General Guidelines
+
+**Workflow Principles**:
+- **Start with templates** - Use predefined templates for consistency
+- **Be specific** - Clear PURPOSE, TASK, and EXPECTED fields
+- **Include constraints** - File patterns, scope, requirements in RULES
+- **Discover patterns first** - Use rg/MCP for complex file discovery before CLI execution
+- **Build precise CONTEXT** - Convert discovery results to explicit file references
+- **Document context** - Always reference CLAUDE.md for context
+- **Default to full context** - Use `@**/*` in CONTEXT for comprehensive analysis unless specific files needed
+- **⚠️ No escape characters in CLI commands** - NEVER use `\$`, `\"`, `\'` in actual CLI execution (breaks command substitution and path expansion)
+
+---
+
+### Context Optimization Strategy
+
+**Directory Navigation**: Use `cd [directory] &&` pattern when analyzing specific areas to reduce irrelevant context
+
+**When to change directory**:
+- Specific directory mentioned → Use `cd directory &&` pattern
+- Focused analysis needed → Target specific directory with cd
+- Multi-directory scope → Use `cd` + `--include-directories` for precise control
+
+**When to use `--include-directories`**:
+- Working in subdirectory but need parent/sibling context
+- Cross-directory dependency analysis required
+- Multiple related modules need simultaneous access
+
+---
 
 ### Workflow Integration (REQUIRED)
+
 When planning any coding task, **ALWAYS** integrate CLI tools:
 
 1. **Understanding Phase**: Use Gemini for analysis (Qwen as fallback)
@@ -319,185 +461,16 @@ When planning any coding task, **ALWAYS** integrate CLI tools:
 3. **Implementation Phase**: Use Codex for development
 4. **Quality Phase**: Use Codex for testing and validation
 
-### Common Scenarios
-
-#### Code Analysis
-```bash
-~/.claude/scripts/gemini-wrapper -p "
-PURPOSE: Understand codebase architecture
-TASK: Analyze project structure and identify patterns
-MODE: analysis
-CONTEXT: @{src/**/*.ts,CLAUDE.md} Previous analysis of auth system
-EXPECTED: Architecture overview and integration points
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/architecture.txt) | Focus on integration points
-"
-```
-
-#### Documentation Generation
-```bash
-~/.claude/scripts/gemini-wrapper -p "
-PURPOSE: Generate API documentation
-TASK: Create comprehensive API reference from code
-MODE: write
-CONTEXT: @{src/api/**/*}
-EXPECTED: API.md with all endpoints documented
-RULES: Follow project documentation standards
-"
-```
-
-#### Architecture Analysis (Qwen as Gemini fallback)
-```bash
-# Prefer Gemini for architecture analysis
-cd src/auth && ~/.claude/scripts/gemini-wrapper -p "
-PURPOSE: Analyze authentication system architecture
-TASK: Review JWT-based auth system design
-MODE: analysis
-CONTEXT: @{src/auth/**/*} Existing patterns and requirements
-EXPECTED: Architecture analysis report with recommendations
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/architecture.txt) | Focus on security
-"
-
-# Use Qwen only if Gemini unavailable
-cd src/auth && ~/.claude/scripts/qwen-wrapper -p "
-PURPOSE: Analyze authentication system architecture
-TASK: Review JWT-based auth system design
-MODE: analysis
-CONTEXT: @{src/auth/**/*} Existing patterns and requirements
-EXPECTED: Architecture analysis report with recommendations
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/architecture.txt) | Focus on security
-"
-```
-
-#### Feature Development (Multi-task with Resume)
-```bash
-# First task - establish session
-codex -C path/to/project --full-auto exec "
-PURPOSE: Implement user authentication
-TASK: Create JWT-based authentication system
-MODE: auto
-CONTEXT: @{src/auth/**/*} Database schema from session memory
-EXPECTED: Complete auth module with tests
-RULES: $(cat ~/.claude/workflows/cli-templates/prompts/development/feature.txt) | Follow security best practices
-" --skip-git-repo-check -s danger-full-access
-
-# Continue in same session - Add JWT validation
-codex --full-auto exec "
-PURPOSE: Enhance authentication security
-TASK: Add JWT token validation and refresh logic
-MODE: auto
-CONTEXT: Previous auth implementation from current session
-EXPECTED: JWT validation middleware and token refresh endpoints
-RULES: Follow JWT best practices, maintain session context
-" resume --last --skip-git-repo-check -s danger-full-access
-
-# Continue in same session - Add tests
-codex --full-auto exec "
-PURPOSE: Increase test coverage
-TASK: Generate comprehensive tests for auth module
-MODE: write
-CONTEXT: Auth implementation from current session
-EXPECTED: Complete test suite with 80%+ coverage
-RULES: Use Jest, follow existing patterns
-" resume --last --skip-git-repo-check -s danger-full-access
-```
-
-#### Interactive Session Resume
-```bash
-# Resume previous session with picker
-codex resume
-
-# Or resume most recent session directly
-codex resume --last
-```
-
 ---
 
-## 🔧 Best Practices
-
-### General Guidelines
-- **Start with templates** - Use predefined templates for consistency
-- **Be specific** - Clear PURPOSE, TASK, and EXPECTED fields
-- **Include constraints** - File patterns, scope, requirements in RULES
-- **Discover patterns first** - Use rg/MCP for complex file discovery before CLI execution
-- **Build precise CONTEXT** - Convert discovery results to explicit file references
-- **Document context** - Always reference CLAUDE.md for context
-- **⚠️ No escape characters in CLI commands** - NEVER use `\$`, `\"`, `\'` in actual CLI execution (breaks command substitution and path expansion)
-
-### Context Optimization Strategy
-**Directory Navigation**: Use `cd [directory] &&` pattern when analyzing specific areas to reduce irrelevant context
-
-**When to change directory**:
-- Specific directory mentioned → Use `cd directory &&` pattern
-- Focused analysis needed → Target specific directory with cd
-- Multi-directory scope → Stay in root, use explicit paths or multiple commands
-
-**Example**:
-```bash
-# Gemini - Focused analysis
-cd src/auth && ~/.claude/scripts/gemini-wrapper -p "
-PURPOSE: Understand authentication patterns
-TASK: Analyze auth implementation
-MODE: analysis
-CONTEXT: @{**/*.ts}
-EXPECTED: Pattern documentation
-RULES: Focus on security best practices
-"
-
-# Qwen - Analysis (fallback option, same as Gemini)
-cd src/auth && ~/.claude/scripts/qwen-wrapper -p "
-PURPOSE: Analyze auth architecture
-TASK: Review auth system design and patterns
-MODE: analysis
-CONTEXT: @{**/*}
-EXPECTED: Architecture analysis report
-RULES: Focus on modularity and security
-"
-
-# Codex - Implementation
-codex -C src/auth --full-auto exec "
-PURPOSE: Improve auth implementation
-TASK: Review and enhance auth code
-MODE: auto
-CONTEXT: @{**/*.ts}
-EXPECTED: Code improvements and fixes
-RULES: Maintain backward compatibility
-" --skip-git-repo-check -s danger-full-access
-```
-
 ### Planning Checklist
 
 For every development task:
 - [ ] **Purpose defined** - Clear goal and intent
 - [ ] **Mode selected** - Execution mode and permission level determined
-- [ ] **Context gathered** - File references and session memory documented
+- [ ] **Context gathered** - File references and session memory documented (default `@**/*`)
+- [ ] **Directory navigation** - Determine if `cd` or `cd + --include-directories` needed
 - [ ] **Gemini analysis** completed for understanding
 - [ ] **Template selected** - Appropriate template chosen
 - [ ] **Constraints specified** - File patterns, scope, requirements
 - [ ] **Implementation approach** - Tool selection and workflow
-- [ ] **Quality measures** - Testing and validation plan
-- [ ] **Tool configuration** - Review `.gemini/CLAUDE.md` or `.codex/Agent.md` if needed
-
----
-
-## ⚙️ Execution Configuration
-
-### Core Execution Rules
-- **Dynamic Timeout (20-120min)**: Allocate execution time based on task complexity
-  - Simple tasks (analysis, search): 20-40min (1200000-2400000ms)
-  - Medium tasks (refactoring, documentation): 40-60min (2400000-3600000ms)
-  - Complex tasks (implementation, migration): 60-120min (3600000-7200000ms)
-- **Codex Multiplier**: Codex commands use 1.5x of allocated time
-- **Apply to All Tools**: All bash() wrapped commands including Gemini, Qwen wrapper and Codex executions
-- **Command Examples**: `bash(~/.claude/scripts/gemini-wrapper -p "prompt")`, `bash(codex -C directory --full-auto exec "task")`
-- **Auto-detect**: Analyze PURPOSE and TASK fields to determine appropriate timeout
-
-### Permission Framework
-- **⚠️ WRITE PROTECTION**: Local codebase write/modify requires EXPLICIT user confirmation
-  - **Analysis Mode (default)**: Read-only, safe for auto-execution
-  - **Write Mode**: Requires user explicitly states MODE=write or MODE=auto in prompt
-  - **Exception**: User provides clear instructions like "modify", "create", "implement"
-- **Gemini/Qwen Write Access**: Use `--approval-mode yolo` ONLY when MODE=write explicitly specified
-  - **Parameter Position**: Place AFTER the wrapper command: `gemini-wrapper --approval-mode yolo -p "..."`
-- **Codex Write Access**: Use `-s danger-full-access` and `--skip-git-repo-check` ONLY when MODE=auto explicitly specified
-  - **Parameter Position**: Place AFTER the prompt string at command END: `codex ... exec "..." --skip-git-repo-check -s danger-full-access`
-- **Default Behavior**: All tools default to analysis/read-only mode without explicit write permission

.claude/workflows/mcp-tool-strategy.md

@@ -86,9 +86,9 @@ mcp__code-index__search_code_advanced(pattern="async.*function", file_pattern="*
 mcp__exa__get_code_context_exa(query="TypeScript async patterns", tokensNum="dynamic")
 
 # 3. Analyze with Gemini
-cd "src/async" && ~/.claude/scripts/gemini-wrapper -p "
+cd "src/async" && gemini "
 PURPOSE: Understand async patterns
-CONTEXT: Code index results + Exa context + @{src/async/**/*}
+CONTEXT: Code index results + Exa context + @src/async/**/*
 EXPECTED: Pattern analysis
 RULES: Focus on TypeScript best practices
 "
@@ -134,7 +134,7 @@ codex -C src/async --full-auto exec "Apply modern async patterns" -s danger-full
 mcp__code-index__search_code_advanced(pattern="router|routing", file_pattern="*.ts")
 mcp__exa__get_code_context_exa(query="Next.js 14 app router", tokensNum="dynamic")
 mcp__exa__web_search_exa(query="Next.js 14 best practices 2024", numResults=3)
-cd "src/app" && ~/.claude/scripts/gemini-wrapper -p "Learn Next.js patterns"
+cd "src/app" && gemini "Learn Next.js patterns"
 ```
 
 ### Debugging
@@ -153,7 +153,7 @@ mcp__code-index__refresh_index()  # 刷新索引
 mcp__code-index__find_files(pattern="*auth*")  # Find auth-related files
 mcp__code-index__search_code_advanced(pattern="function.*auth", file_pattern="*.ts")  # Find auth functions
 mcp__code-index__get_file_summary(file_path="src/auth/index.ts")  # Understand structure
-cd "src/auth" && ~/.claude/scripts/gemini-wrapper -p "Analyze auth architecture"
+cd "src/auth" && gemini "Analyze auth architecture"
 ```
 
 ### Project Setup Workflow

.claude/workflows/workflow-architecture.md

@@ -152,7 +152,7 @@ All task files use this unified 5-field schema with optional artifacts enhanceme
       {
         "step": "analyze_architecture",
         "action": "Review system architecture",
-        "command": "~/.claude/scripts/gemini-wrapper -p \"analyze patterns: [patterns]\"",
+        "command": "gemini \"analyze patterns: [patterns]\"",
         "output_to": "design"
       },
       {
@@ -416,7 +416,7 @@ The `[FLOW_CONTROL]` marker indicates that a task or prompt contains flow contro
 - **Bash commands**: `bash(command)` - Any shell command
 - **Tool calls**: `Read(file)`, `Glob(pattern)`, `Grep(pattern)`
 - **MCP tools**: `mcp__code-index__find_files()`, `mcp__exa__get_code_context_exa()`
-- **CLI wrappers**: `~/.claude/scripts/gemini-wrapper`, `codex --full-auto exec`
+- **CLI commands**: `gemini`, `qwen`, `codex --full-auto exec`
 
 **Example**:
 ```json
@@ -477,10 +477,10 @@ The `[FLOW_CONTROL]` marker indicates that a task or prompt contains flow contro
 "command": "codex --full-auto exec \"task\" resume --last --skip-git-repo-check -s danger-full-access"
 
 // Gemini (user requested)
-"command": "~/.claude/scripts/gemini-wrapper -p \"analyze [context]\""
+"command": "gemini \"analyze [context]\""
 
 // Qwen (fallback for Gemini)
-"command": "~/.claude/scripts/qwen-wrapper -p \"analyze [context]\""
+"command": "qwen \"analyze [context]\""
 ```
 
 **Example Step**:
@@ -517,14 +517,14 @@ The `[FLOW_CONTROL]` marker indicates that a task or prompt contains flow contro
 
 **Gemini CLI**:
 ```bash
-~/.claude/scripts/gemini-wrapper -p "prompt"
+gemini "prompt"
-~/.claude/scripts/gemini-wrapper --approval-mode yolo -p "prompt"  # For write mode
+gemini --approval-mode yolo "prompt"  # For write mode
 ```
 
 **Qwen CLI** (Gemini fallback):
 ```bash
-~/.claude/scripts/qwen-wrapper -p "prompt"
+qwen "prompt"
-~/.claude/scripts/qwen-wrapper --approval-mode yolo -p "prompt"  # For write mode
+qwen --approval-mode yolo "prompt"  # For write mode
 ```
 
 **Codex CLI**:
@@ -892,13 +892,13 @@ fi
 - **Examples**: New features, API endpoints with integration, database schema changes
 - **Task Decomposition**: Two-level hierarchy when decomposition is needed
 - **Agent Coordination**: Context coordination between related tasks
-- **Tool Strategy**: `gemini-wrapper` for pattern analysis, `codex --full-auto` for implementation
+- **Tool Strategy**: `gemini` for pattern analysis, `codex --full-auto` for implementation
 
 #### Complex Workflows
 - **Examples**: Major features, architecture refactoring, security implementations, multi-service deployments
 - **Task Decomposition**: Frequent use of two-level hierarchy with dynamic subtask creation
 - **Agent Coordination**: Multi-agent orchestration with deep context analysis
-- **Tool Strategy**: `gemini-wrapper` for architecture analysis, `codex --full-auto` for complex problem solving, `bash()` commands for flexible analysis
+- **Tool Strategy**: `gemini` for architecture analysis, `codex --full-auto` for complex problem solving, `bash()` commands for flexible analysis
 
 ### Assessment & Upgrades
 - **During Creation**: System evaluates requirements and assigns complexity