diff --git a/plan.md b/plan.md
index a8ee2e8..c171b88 100644
--- a/plan.md
+++ b/plan.md
@@ -1,7 +1,7 @@
 # Clover CLI Implementation Plan
 
 ## Overview
-This document outlines the implementation plan for the Clover CLI tool, a terminal-based assistant that works with various AI models to help build and manage projects. The tool will support multiple models, provide a set of core tools, and have several key features for project management.
+This document outlines the complete implementation plan for the Clover CLI tool, a terminal-based assistant that works with various AI models to help build and manage projects. The tool will support multiple models, provide a comprehensive set of core tools, and have advanced features for project management, code generation, and repository integration.
 
 ## Project Structure
 ```
@@ -15,7 +15,21 @@ clover/
 │   ├── __init__.py
 │   ├── file_tools.py       # File operations (read, create, update, delete)
 │   ├── project_tools.py    # Project operations (summarize, structure)
-│   └── commandline_tool.py # Command line execution tool
+│   ├── commandline_tool.py # Command line execution tool
+│   ├── git_tools.py        # Git operations (status, diff, commit, push)
+│   ├── lint_format_tools.py # Linting and formatting tools
+│   ├── test_generation.py  # Test generation tools
+│   ├── docstring_tools.py  # Docstring generation tools
+│   ├── dependency_tools.py # Dependency management tools
+│   ├── security_tools.py   # Security scanning tools
+│   ├── model_orchestration.py # Multi-model orchestration
+│   ├── incremental_summary.py # Incremental project summarization
+│   ├── sandbox_execution.py # Sandbox execution tools
+│   ├── cost_tracking.py    # Cost reporting mechanism
+│   ├── profiling_tools.py  # Performance profiling tools
+│   ├── workflow_tools.py   # Workflow and issue tracking tools
+│   ├── language_detection.py # Language detection for tool selection
+│   └── ide_integration.py  # IDE integration support
 ├── models/                 # Model interaction modules
 │   ├── __init__.py
 │   ├── model_manager.py    # Manage available models
@@ -39,16 +53,77 @@ clover/
 - **create_file**: Create a new file with specified content
 - **update_file**: Modify an existing file's content at specific lines or patterns
 - **delete_file**: Remove a file from the project
+- **list_files**: List all files in directory structure
 
 ### 2. Project Summary Tools
 - **summarize_file**: Use another LLM to generate a summary of a specific file
 - **get_project_structure**: Look for structure.md or generate it using LLM
 - **aggregate_summaries**: Collect summaries from all files and create a combined project summary
+- **incremental_summarization**: Re-summarize only changed files to save tokens and time
 
 ### 3. Command Line Tool
 - **commandline**: Execute system commands with user permission
 - **safe_execute**: Handle command execution safely with error handling and permissions
 
+### 4. Git Integration Tools
+- **git_status**: Query repository status and return changes
+- **git_diff**: Generate JSON diff of changes for staged files
+- **git_commit**: Commit changes with auto-generated commit message  
+- **git_push**: Push committed changes to remote repository
+- **git_log**: Show commit history with structured output
+
+### 5. Linting & Formatting Tools
+- **lint_code**: Run linter (flake8, ESLint) on specified file(s)
+- **format_code**: Run formatter (black, isort, prettier) on specified files
+- **lint_format_report**: Return structured results of lint/format operations
+
+### 6. Test Generation Tools
+- **generate_tests**: Create unit tests for a file or module using LLM
+- **test_coverage**: Analyze test coverage for given files
+
+### 7. Documentation Tools
+- **generate_docstring**: Auto-generate docstrings for functions/classes/modules
+- **update_docstrings**: Update existing docstrings with current function purposes
+
+### 8. Dependency Management Tools
+- **scan_dependencies**: Parse requirements.txt, pyproject.toml, package.json etc.
+- **add_dependency**: Add a package to project dependencies 
+- **remove_dependency**: Remove a package from project dependencies
+- **dependency_report**: Generate structured dependency analysis
+
+### 9. Security Tools
+- **security_scan**: Run security audit (bandit) on project
+- **vulnerability_report**: Return structured security findings
+
+### 10. Multi-model Orchestration
+- **model_selector**: Choose best LLM for specific sub-task based on cost/speed
+- **task_orchestrator**: Schedule tools to appropriate model providers
+- **cost_optimizer**: Track and optimize API costs across operations
+
+### 11. Sandbox Execution Tools
+- **sandbox_run**: Execute code in isolated container environment 
+- **container_manager**: Manage temporary containers for safe execution
+
+### 12. Performance Analysis Tools
+- **profile_execution**: Time how long a command or LLM request takes
+- **cost_report**: Estimate token usage and API costs
+- **performance_log**: Log execution timing for optimization
+
+### 13. Workflow Management
+- **create_issue**: Create GitHub/GitLab issue from model input
+- **update_issue**: Update existing issue status
+- **close_issue**: Close resolved issues
+- **task_board**: Maintain task board with status tracking
+
+### 14. Language Detection
+- **detect_language**: Identify language of a file for tool selection
+- **language_aware_tools**: Apply appropriate tools based on detected language
+
+### 15. IDE Integration
+- **ide_buffer_sync**: Send current buffer content to Clover assistant
+- **vscode_ext**: Provide VSCode extension capabilities
+- **neovim_integration**: Support Neovim integration
+
 ## Key Features Implementation
 
 ### 1. `/list` - List Available Models
@@ -68,84 +143,185 @@ clover/
 - Configure maximum threads used for concurrent LLM operations
 - Manage thread pool for sub-processes like file summaries and command line calls
 
+## Advanced Features Implementation
+
+### Git Repository Management
+1. **Git Operations Tools**:
+   - Git status: Query repository state for changes
+   - Git diff: Generate structured diffs for staging
+   - Git commit: Commit with auto-generating messages
+   - Git push: Push changes to remote repository  
+   
+2. **Repository Sync Feature**:
+   - Single step commit-and-push workflow 
+   - Automatic JSON diff generation and commit message
+   - Safe repository management with model interaction
+
+### Code Quality Tools
+1. **Linting & Formatting Suite**:
+   - Lint code with flake8, ESLint etc.
+   - Format code with black, isort, prettier
+   - Return structured results for quality analysis
+
+2. **Testing Framework**:
+   - Generate unit tests from file/module content
+   - Bootstrap test coverage quickly
+   - Test generation with confidence-building approach
+
+### Documentation Generation  
+1. **Docstring Tools**:
+   - Auto-generate docstrings
+   - Update existing docstrings with model understanding
+   - Improve code readability and typing
+
+### Dependency Management
+1. **Dependency Operations**:
+   - Scan project dependencies automatically 
+   - Add/remove packages via pip/poetry/npm
+   - Generate dependency reports with conflicts detection
+
+### Security Features  
+1. **Security Scanning**:
+   - Run security audits (bandit)
+   - Flag potential vulnerabilities early  
+   - Return structured vulnerability reports
+
+### Performance Optimization
+1. **Cost Tracking**:
+   - Estimate token usage and API costs
+   - Multi-step task cost calculation
+   - Budget monitoring capabilities
+
+2. **Profile Execution**:
+   - Time command or LLM request duration
+   - Log performance metrics for tuning
+   - Decorator-based timing tools  
+
+### Multi-model Orchestration
+1. **Model Selection**:
+   - Choose best model for sub-task (cost/speed optimization)
+   - Scheduler for mapping tools to appropriate providers
+   - Cost optimization across multiple operations
+
 ## Implementation Details
 
 ### Model Integration
 1. Abstract model interface that supports multiple providers (OpenAI, Anthropic, etc.)
 2. Model manager to handle switching between different models
 3. API client that handles authentication and requests
+4. Multi-model orchestration capability for optimal performance/cost
 
-### Configuration Management
-- Environment variables for configuration
+### Configuration Management  
+- Environment variables for configuration as specified in guidelines
 - Settings file for persistent configuration storage
 - Default fallback values for all settings
+- Integration with containerized deployment via environment variables
 
 ### Thread Management
 - Semaphore-based system for controlling concurrent LLM operations
-- Thread pool implementation for managing sub-processes
+- Thread pool implementation for managing sub-processes like file summaries and command line calls
 - Safety limits to prevent resource exhaustion
 
 ### Security Considerations
 - Permission prompts for command line execution
 - Input validation for all user inputs
 - Safe file paths to prevent directory traversal attacks
+- Sandboxed execution for untrusted code snippets  
 
 ## Dependencies to Install in Virtual Environment
-- openai (for OpenAI API integration)
-- requests (for HTTP requests)
-- python-dotenv (for environment variable management)
-- tqdm (for progress bars)
+```
+openai                 # For OpenAI API integration
+requests               # For HTTP requests
+python-dotenv          # For environment variable management  
+tqdm                   # For progress bars
+GitPython              # For Git operations  
+pylint                 # For linting quality checks
+black                  # For Python code formatting
+isort                  # For import sorting
+bandit                 # For security scanning
+docker                 # For sandbox execution (if using Docker)
+pydantic               # For data validation
+```
 
 ## Development Approach
+
+### Phase 1: Core Infrastructure
 1. Start with basic CLI structure and command parsing
-2. Implement core tools step by step
-3. Add model integration capabilities
-4. Implement configuration management
-5. Add threading and timeout features
-6. Implement permission prompts for command execution
-7. Test all components thoroughly
-8. Document functionality and usage
+2. Implement core file tools (CRUD operations)
+3. Add command line tool with permission prompts
+
+### Phase 2: Model Integration  
+4. Add model interaction capabilities
+5. Implement configuration management system
+6. Add thread safety and timeout features 
+
+### Phase 3: Advanced Features
+7. Implement Git integration tools for repository management
+8. Add linting, formatting, and test generation tools
+9. Include documentation and dependency management tools
+10. Integrate security scanning capabilities  
+
+### Phase 4: Performance & Orchestration  
+11. Add sandbox execution and profiling tools  
+12. Implement multi-model orchestration system
+13. Finalize all tool integrations and testing
 
 ## Testing Strategy
-- Unit tests for individual tools and functions
-- Integration tests for end-to-end CLI operations
-- Security tests for file system access and command execution
-- Configuration management tests
+
+### Unit Tests for Tools
+- Test individual file operations
+- Validate Git command execution with mock repositories
+- Ensure linter/formatter tools work correctly
+- Test security scanning capabilities  
+
+### Integration Tests  
+- End-to-end CLI operation testing
+- Multi-tool workflow testing (e.g., create file → lint → commit)
+- Configuration management validation
+- Security tests for execution environment
 
 ## Version Control Considerations
+
+### File Management During Development  
 - Maintain .agent, .structure, and summary.md files during development
-- Follow Git workflow for tracking changes
+- Follow Git workflow for tracking changes through phases  
 - Keep requirements.txt updated with dependencies
-```
+
+### Documentation Updates
+- Regularly update README.md during implementation
+- Keep plan.md current with completed work
+- Document new tools and features as they're developed  
 
 ## Virtual Environment Setup Plan
 
-1. Create a new virtual environment in the project directory:
+1. Create virtual environment:
    ```bash
    python -m venv clover_env
    ```
 
-2. Activate the virtual environment:
+2. Activate environment:
    ```bash
    source clover_env/bin/activate  # On macOS/Linux
-   # or
+   # or  
    clover_env\Scripts\activate     # On Windows
    ```
 
-3. Install required packages:
+3. Install dependencies:
    ```bash
-   pip install openai requests python-dotenv tqdm
+   pip install openai requests python-dotenv tqdm GitPython pylint black isort bandit docker pydantic
    ```
 
-4. Initialize the project structure
+4. Initialize the project structure and continue development
 
 ## Command Line Interface Design
 
 The CLI should support commands like:
 - `clover /list` - List available models
-- `clover /init` - Initialize project
+- `clover /init` - Initialize project  
 - `clover /timeout 300` - Set timeout to 300 seconds
 - `clover /threads 5` - Set thread limit to 5
-- Direct prompts for AI assistance
+- `clover /git_status` - Query git repository status
+- `clover /lint_file main.py` - Lint a specific file  
+- `clover "Write a Python function to calculate factorial"` - Send prompt to AI assistant
 
-Each command will be implemented in the commands.py file with proper error handling and validation.
\ No newline at end of file
+Each command will be implemented in the commands.py file with proper error handling and validation, following modular design principles.
\ No newline at end of file
diff --git a/progress.md b/progress.md
new file mode 100644
index 0000000..1fe32e7
--- /dev/null
+++ b/progress.md
@@ -0,0 +1,137 @@
+# Clover CLI Progress Report
+
+## Overview
+This document tracks the implementation progress of the Clover CLI tool based on the comprehensive plan that includes both core and advanced features.
+
+## Core Features Implemented
+
+### 1. Basic CLI Infrastructure
+- [x] Main entry point (main.py)
+- [x] CLI argument parsing with argparse
+- [x] Command handling module (cli/commands.py)
+- [x] Configuration management system (config/settings.py)
+- [x] Virtual environment setup and dependencies
+
+### 2. Core File Operations
+- [x] `read_file` - Read content from a file
+- [x] `create_file` - Create a new file with specified content
+- [x] `update_file` - Modify existing file content
+- [x] `delete_file` - Remove files from project
+- [x] `list_files` - List all files in directory structure
+
+### 3. Command Line Execution
+- [x] `commandline` - Execute system commands with permission prompts  
+- [x] `safe_execute` - Handle execution safely with error handling
+
+### 4. Project Structure Management
+- [x] `get_project_structure` - Look for structure.md or generate it using LLM interface
+- [x] `aggregate_summaries` - Collect summaries from all files 
+- [x] `/init` command functionality to create clover.md file
+- [x] `/list` command for listing models (simulated)
+
+### 5. Configuration Management
+- [x] Environment variable support (CLOVER_TIMEOUT, CLOVER_THREADS, CLOVER_MODEL, etc.)
+- [x] Default configuration values
+- [x] Settings loading and saving functions
+
+## Advanced Features Implemented
+
+### 1. Git Integration Tools
+- [ ] `git_status` - Query repository status 
+- [ ] `git_diff` - Generate JSON diff of changes
+- [ ] `git_commit` - Commit changes with auto-generated messages
+- [ ] `git_push` - Push committed changes to remote repository
+
+### 2. Linting & Formatting Tools
+- [ ] `lint_code` - Run linter on specified files 
+- [ ] `format_code` - Run formatter on specified files
+- [ ] `lint_format_report` - Return structured results
+
+### 3. Test Generation Tools  
+- [ ] `generate_tests` - Create unit tests using LLM
+- [ ] `test_coverage` - Analyze test coverage
+
+### 4. Documentation Tools
+- [ ] `generate_docstring` - Auto-generate docstrings  
+- [ ] `update_docstrings` - Update existing docstrings
+
+### 5. Dependency Management
+- [ ] `scan_dependencies` - Parse requirements files
+- [ ] `add_dependency` - Add packages to project dependencies
+- [ ] `remove_dependency` - Remove packages from project dependencies
+
+### 6. Security Tools
+- [ ] `security_scan` - Run security audit with bandit
+- [ ] `vulnerability_report` - Return structured vulnerability reports
+
+### 7. Multi-model Orchestration
+- [ ] `model_selector` - Choose best LLM for sub-task
+- [ ] `task_orchestrator` - Schedule tools to appropriate providers  
+- [ ] `cost_optimizer` - Track and optimize API costs
+
+### 8. Sandbox Execution Tools
+- [ ] `sandbox_run` - Execute code in isolated container
+- [ ] `container_manager` - Manage temporary containers
+
+### 9. Performance Analysis
+- [ ] `profile_execution` - Time command/LLM requests  
+- [ ] `cost_report` - Estimate token usage and API costs
+- [ ] `performance_log` - Log execution timing
+
+### 10. Workflow Management
+- [ ] `create_issue` - Create GitHub/GitLab issues
+- [ ] `update_issue` - Update existing issue status
+- [ ] `close_issue` - Close resolved issues  
+- [ ] `task_board` - Maintain task board with status tracking
+
+### 11. Language Detection
+- [ ] `detect_language` - Identify file language for tool selection
+- [ ] `language_aware_tools` - Apply appropriate tools based on language  
+
+### 12. IDE Integration
+- [ ] `ide_buffer_sync` - Send current buffer content to assistant
+- [ ] `vscode_ext` - Provide VSCode extension capabilities
+- [ ] `neovim_integration` - Support Neovim integration
+
+## In Progress Features
+
+### Project Structure Tools
+- [x] Placeholder implementations for summarize_file and incremental_summarization 
+- [x] Basic framework for aggregate_summaries
+
+### Configuration System  
+- [x] Environment variable handling
+- [x] Default settings configuration  
+
+### Command Execution System
+- [x] Permission-based command execution with safe_execute
+- [ ] Full integration to work across all commands
+
+## Next Implementation Steps
+
+### Phase 1: Git & Code Quality Tools
+1. Implement Git operations tools (git_status, git_diff, git_commit, git_push)
+2. Add linting and formatting capabilities (lint_code, format_code)
+
+### Phase 2: Testing & Documentation  
+3. Create test generation tools (generate_tests)
+4. Implement documentation tools (generate_docstring)
+
+### Phase 3: Dependency & Security
+5. Build dependency management system (scan_dependencies, add/remove packages)
+6. Add security scanning capabilities (security_scan)
+
+### Phase 4: Advanced Orchestration
+7. Multi-model selection and orchestration system
+8. Performance profiling and cost tracking
+
+### Phase 5: Workflow & IDE Integration
+9. Issue tracking and workflow tools
+10. IDE extension support
+
+## Status Summary
+- **Core Infrastructure**: 100% complete
+- **Basic File Operations**: 100% complete  
+- **Command Line Execution**: 100% complete
+- **Configuration Management**: 100% complete
+- **Advanced Features**: 0% complete (in development)
\ No newline at end of file