Issue #11: Documentation Completion

### Issue #11: Documentation Completion

**Priority:** Medium

**Estimated Time:** 3 days

**Detailed Description:**
Complete all documentation, including the README, CLI help text, and user guides.

**Implementation Details:**

1. Update the main [README.md](http://readme.md/):

```markdown
# Malware Minimizer

A cross-platform, open-source command-line tool for scanning, detecting, quarantining, and removing malware.

## Features

- **Fast Scan**: Efficiently detect known malware using signature-based scanning
- **Deep Scan**: Find suspicious files using heuristic analysis
- **Quarantine**: Safely isolate potentially malicious files
- **One-Command Installation**: Install directly from your terminal
- **Cross-Platform**: Works on Windows, macOS, and Linux
- **Free & Open Source**: Never pay for basic malware protection again

## Quick Installation

### Linux/macOS

```bash
curl -s https://raw.githubusercontent.com/Jordan231111/MalwareMinimizer/main/scripts/install.sh | bash

```

### Windows (PowerShell as Administrator)

```powershell
Invoke-WebRequest -Uri "https://raw.githubusercontent.com/Jordan231111/MalwareMinimizer/main/scripts/install.ps1" -OutFile "$env:TEMP\install.ps1"; powershell -ExecutionPolicy Bypass -File "$env:TEMP\install.ps1"

```

### Direct Usage (No Installation)

For Linux/macOS, you can run the tool directly without installing:

```bash
curl -s https://raw.githubusercontent.com/Jordan231111/MalwareMinimizer/main/scripts/run_direct.sh | bash -- --help

```

## Basic Usage

### Scanning for Malware

```bash
# Fast scan (signature-based)
malware_minimizer scan --path /path/to/scan

# Deep scan (with heuristics)
malware_minimizer scan --path /path/to/scan --deep

```

### Managing Threats

```bash
# List quarantined files
malware_minimizer list-quarantined

# Quarantine a file
malware_minimizer quarantine-file --path /path/to/suspicious/file

# Restore a quarantined file
malware_minimizer restore --id <quarantine_id>

# Remove a quarantined file
malware_minimizer remove --id <quarantine_id>

# Remove a file directly
malware_minimizer remove-file --path /path/to/malicious/file

```

### Updating Signature Database

```bash
# Update malware definitions
malware_minimizer update-db

# Set up scheduled updates
malware_minimizer schedule-updates --hours 24

```

## How It Works

### Fast Scan

The Fast Scan calculates SHA-256 hashes of files and compares them against our database of known malware signatures. This is very efficient and has virtually no false positives, but can only detect previously identified threats.

### Deep Scan

The Deep Scan uses heuristic analysis to identify suspicious files:

- **High Entropy**: Detects encrypted or packed files
- **Extension Mismatch**: Finds files disguising their true type
- **Suspicious Patterns**: Identifies potentially malicious code
- **Known Packer Signatures**: Detects common obfuscation techniques
- **Unusual Locations**: Flags executables in suspicious directories

## Security & Privacy

- All scanning happens locally on your device
- No data is sent to external servers (except database updates)
- Quarantined files are stored securely with restricted permissions
- Installation scripts verify file integrity with SHA-256 checksums

## Building from Source

### Requirements

- Rust (nightly toolchain)
- Cargo

```bash
# Clone the repository
git clone https://github.com/Jordan231111/MalwareMinimizer.git
cd MalwareMinimizer

# Build the project
cargo build --release

# Run the binary
./target/release/malware_minimizer --help

```

## Detailed Documentation

For complete documentation, see:

- [[CLI User Guide](https://claude.ai/chat/docs/CLI_USER_DOC.md)](https://claude.ai/chat/docs/CLI_USER_DOC.md)
- [[Contributing Guidelines](https://claude.ai/chat/CONTRIBUTING.md)](https://claude.ai/chat/CONTRIBUTING.md)

## License

This project is licensed under the GNU General Public License v3.0 - see the [[LICENSE](https://claude.ai/chat/LICENSE)](https://claude.ai/chat/LICENSE) file for details.

## Acknowledgments

- [insert acknowledgments here]

```

2. Update `docs/CLI_USER_DOC.md`:
```markdown
# MalwareMinimizer CLI Documentation

## Table of Contents

- [Overview](#overview)
- [Commands Reference](#commands-reference)
  - [Scan Command](#scan-command)
  - [Update Database](#update-database)
  - [Quarantine Commands](#quarantine-commands)
  - [Remove Commands](#remove-commands)
- [Usage Examples](#usage-examples)
- [Troubleshooting](#troubleshooting)

## Overview

MalwareMinimizer is a command-line tool for scanning, detecting, quarantining, and removing malware. It's designed to be simple, efficient, and cross-platform.

### Installation

For installation instructions, see the [README.md](../README.md) file.

## Commands Reference

### Scan Command

The `scan` command examines files and directories for malware.

```

malware_minimizer scan --path <PATH> [--deep]

```

Options:
- `--path, -p <PATH>`: Directory or file to scan (required)
- `--deep, -d`: Perform heuristic analysis in addition to signature matching

The scan command will:
1. Search for files in the specified path
2. Calculate SHA-256 hashes for each file
3. Compare hashes against the malware database
4. If `--deep` is specified, analyze files using heuristic techniques
5. Display results showing malicious or suspicious files

### Update Database

```

malware_minimizer update-db [--force]

```

Options:
- `--force, -f`: Force update even if the database is current

This command updates the malware signature database to ensure you have the latest protection.

```

malware_minimizer schedule-updates --hours <INTERVAL>

```

Options:
- `--hours, -h <INTERVAL>`: Hours between updates (default: 24)

This command provides instructions for setting up automatic database updates on your system.

### Quarantine Commands

```

malware_minimizer quarantine --id <ID>

```

Shows information about a quarantined file.

```

malware_minimizer quarantine-file --path <PATH> [--name <NAME>]

```

Quarantines a file by its path.

```

malware_minimizer list-quarantined

```

Lists all quarantined files.

```

malware_minimizer restore --id <ID>

```

Restores a quarantined file to its original location.

### Remove Commands

```

malware_minimizer remove --id <ID> [--force]

```

Permanently removes a quarantined file.

```

malware_minimizer remove-file --path <PATH> [--force]

```

Permanently removes a file by its path.

## Usage Examples

### Basic Scan

To scan your Downloads folder:

```bash
malware_minimizer scan --path ~/Downloads

```

### Deep Scan

To perform a more thorough scan of a specific directory:

```bash
malware_minimizer scan --path C:\Users\username\Documents --deep

```

### Quarantine Workflow

1. First, scan to find malicious files:
    
    ```bash
    malware_minimizer scan --path ~/Downloads --deep
    
    ```
    
2. Quarantine a suspicious file:
    
    ```bash
    malware_minimizer quarantine-file --path ~/Downloads/suspicious_file.exe
    
    ```
    
3. View quarantined files:
    
    ```bash
    malware_minimizer list-quarantined
    
    ```
    
4. Remove or restore based on further analysis:
    
    ```bash
    malware_minimizer remove --id abc123
    # or
    malware_minimizer restore --id abc123
    
    ```
    

## Troubleshooting

### Common Issues

### Database Update Fails

If you can't update the database, try:

```bash
malware_minimizer update-db --force

```

If that fails, ensure you have an internet connection and try again later.

### Permission Denied

On Linux/macOS, if you get permission errors:

```bash
sudo malware_minimizer scan --path /system/path

```

On Windows, run PowerShell as Administrator.

### High False Positive Rate in Deep Scan

Deep Scan uses heuristics which may flag legitimate files. You can:

1. Use Fast Scan instead
2. Examine suspicious files carefully before removing them
3. Use the quarantine feature to test if removing a file causes problems

### Exit Codes

- `0`: Success
- `1`: Error (see error message)

```

3. Create a CONTRIBUTING.md file:
```markdown
# Contributing to MalwareMinimizer

Thanks for considering a contribution to MalwareMinimizer! This document provides guidelines to help make the process smooth and effective.

## Getting Started

1. **Fork the repository** on GitHub
2. **Clone your fork** to your local machine
3. **Set up the development environment** (see below)
4. **Create a branch** for your contribution
5. **Make changes** and **test** them
6. **Submit a pull request**

## Development Environment

### Prerequisites

- Rust (nightly toolchain)
- Cargo
- Python 3.11 (for helper scripts)
- Git

### Setup

```bash
# Install Rust (nightly)
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
rustup default nightly

# Clone the repository
git clone https://github.com/YOUR-USERNAME/MalwareMinimizer.git
cd MalwareMinimizer

# Install development dependencies
cargo install cargo-watch cargo-expand cargo-audit

# Build the project
cargo build

```

## Project Structure

- `src/` - Rust source code
    - `main.rs` - Entry point
    - `scanner/` - Scanning engine
    - `database/` - Database operations
    - `quarantine/` - Quarantine system
    - `utils/` - Utility functions
    - `cli/` - Command handlers
- `python_scripts/` - Python helper scripts
- `scripts/` - Installation and utility scripts
- `tests/` - Integration tests
- `docs/` - Documentation

## Coding Guidelines

### Rust Style

- Follow the [[Rust API Guidelines](https://rust-lang.github.io/api-guidelines/)](https://rust-lang.github.io/api-guidelines/)
- Use `cargo fmt` for formatting
- Address all `clippy` warnings
- Write unit tests for all new functionality
- Provide clear error messages and context

### Git Workflow

1. Create a descriptive branch name:
    - `feature/descriptive-name` for new features
    - `bugfix/issue-description` for bug fixes
    - `docs/what-changed` for documentation updates
2. Make focused commits with clear messages:
    
    ```
    Feature: Add file quarantine system
    
    - Implement QuarantineManager
    - Add CLI commands for quarantine operations
    - Write tests for quarantine functionality
    
    ```
    
3. Reference issue numbers in commits when applicable

## Testing

Run the full test suite before submitting a PR:

```bash
# Run all tests
cargo test

# Run a specific test
cargo test test_name

# Run the end-to-end test script
./tests/e2e_test.sh

```

## Pull Request Process

1. Update documentation to reflect any changes
2. Add or update tests as necessary
3. Ensure all tests pass and the build succeeds
4. Update the [CHANGELOG.md](http://changelog.md/) (if applicable)
5. Submit the PR with a clear description of the changes

## Code of Conduct

- Be respectful and inclusive
- Focus on the technical merits of contributions
- Provide constructive feedback
- Help create a positive community

## License

By contributing to MalwareMinimizer, you agree that your contributions will be licensed under the project's [[GNU GPL v3 License](https://claude.ai/chat/LICENSE)](https://claude.ai/chat/LICENSE).

```

4. Create a SECURITY.md file:
```markdown
# Security Policy

## Reporting a Vulnerability

If you discover a security vulnerability in MalwareMinimizer, please follow these steps:

1. **Do not disclose the vulnerability publicly**
2. Email the details to [your-email@example.com]
3. Include:
   - A description of the vulnerability
   - Steps to reproduce
   - Potential impact
   - Any suggestions for mitigation

We will acknowledge your report within 48 hours and provide an estimated timeline for a fix.

## Supported Versions

Only the latest release receives security updates. Please ensure you're using the most recent version.

## Security Measures

### Checksums

All release binaries include SHA-256 checksums for verification. Always verify the integrity of downloaded files:

```bash
# Linux/macOS
sha256sum -c checksums.txt

# Windows PowerShell
Get-FileHash malware_minimizer_windows.exe | Format-List

```

### Secure Quarantine

Quarantined files are stored with restricted permissions to prevent accidental execution.

### Code Analysis

The project uses:

- Cargo audit for dependency vulnerability checking
- Clippy for static analysis
- Regular dependency updates

## Best Practices

- Keep your installation updated via `malware_minimizer update-db`
- Review quarantined files carefully before restoring them
- Run the tool with appropriate permissions

```

5. Enhance the CLI help text by updating `src/main.rs`:
```rust
// Update the CLI structure with better help text

#[derive(Parser)]
#[command(
    name = "MalwareMinimizer",
    about = "A cross-platform CLI tool to scan, detect, quarantine, and remove malware",
    version,
    author = "Jordan231111 <your-email@example.com>",
    long_about = "MalwareMinimizer provides a simple yet powerful command-line interface for protecting your system from malware. It offers signature-based and heuristic detection, secure quarantine, and safe removal options."
)]
struct Cli {
    /// Increase verbosity (can be used multiple times)
    #[arg(short, long, action = clap::ArgAction::Count, help = "Increase output verbosity: -v for info, -vv for debug, -vvv for trace")]
    verbose: u8,

    #[command(subcommand)]
    command: Commands,
}

#[derive(Subcommand)]
enum Commands {
    /// Scan files or directories for malware
    #[command(
        long_about = "Scans the specified path for malware using signature matching and optionally heuristic analysis.
        Fast scan compares file hashes against a database of known malware signatures.
        Deep scan additionally applies heuristic techniques to detect suspicious files that may not match known signatures."
    )]
    Scan {
        /// Path to scan (file or directory)
        #[arg(short, long, required = true, help = "File or directory to scan")]
        path: String,

        /// Perform deep scan with heuristics
        #[arg(short, long, default_value = "false", help = "Use heuristic analysis to detect suspicious files")]
        deep: bool,
    },

    /// Update the malware signature database
    #[command(
        long_about = "Updates the malware signature database to the latest version.
        The database contains signatures for known malware and is used for fast scanning.
        By default, only updates if a newer version is available."
    )]
    UpdateDb {
        /// Force update even if database is current
        #[arg(short, long, default_value = "false", help = "Force update even if database is current")]
        force: bool,
    },

    /// Schedule automatic database updates
    #[command(
        long_about = "Provides instructions for setting up automatic database updates on your system.
        Different instructions are provided based on your operating system."
    )]
    ScheduleUpdates {
        /// Interval in hours between updates
        #[arg(short, long, default_value = "24", help = "Hours between automatic updates")]
        hours: u64,
    },

    /// Show information about a quarantined file
    #[command(
        long_about = "Displays detailed information about a file in quarantine, including its original path,
        quarantine date, size, hash, and detection information."
    )]
    Quarantine {
        /// ID of the quarantined file
        #[arg(short, long, help = "Quarantine ID from list-quarantined output")]
        id: String,
    },

    /// Quarantine a file by path
    #[command(
        long_about = "Moves a potentially malicious file to the quarantine area.
        The file is stored securely with restricted permissions, and its metadata is preserved.
        You can later restore or permanently remove the file."
    )]
    QuarantineFile {
        /// Path to the file to quarantine
        #[arg(short, long, help = "Path to the file to quarantine")]
        path: String,

        /// Optional malware name for reference
        #[arg(short, long, help = "Optional name or description of the threat")]
        name: Option<String>,
    },

    /// List all quarantined files
    #[command(
        long_about = "Displays a list of all files currently in quarantine, including their IDs,
        original paths, quarantine dates, and detection information."
    )]
    ListQuarantined,

    /// Restore a quarantined file to its original location
    #[command(
        long_about = "Restores a file from quarantine to its original location.
        Use with caution, as this could reintroduce malware to your system.
        Confirmation is required before restoration."
    )]
    Restore {
        /// ID of the quarantined file to restore
        #[arg(short, long, help = "Quarantine ID from list-quarantined output")]
        id: String,
    },

    /// Remove a quarantined file permanently
    #[command(
        long_about = "Permanently deletes a file from quarantine.
        This operation cannot be undone. Confirmation is required unless --force is used."
    )]
    Remove {
        /// ID of the quarantined file to remove
        #[arg(short, long, help = "Quarantine ID from list-quarantined output")]
        id: String,

        /// Force removal without confirmation
        #[arg(short, long, default_value = "false", help = "Skip confirmation prompt")]
        force: bool,
    },

    /// Remove a file directly by path
    #[command(
        long_about = "Permanently deletes a file from the filesystem.
        This operation cannot be undone. Confirmation is required unless --force is used."
    )]
    RemoveFile {
        /// Path to the file to remove
        #[arg(short, long, help = "Path to the file to remove")]
        path: String,

        /// Force removal without confirmation
        #[arg(short, long, default_value = "false", help = "Skip confirmation prompt")]
        force: bool,
    },
}

```

**Acceptance Criteria:**

- README provides clear installation and usage instructions
- CLI_USER_DOC.md covers all commands and options in detail
- [CONTRIBUTING.md](http://contributing.md/) provides clear guidelines for contributors
- [SECURITY.md](http://security.md/) outlines security practices and reporting process
- Command help text is comprehensive and user-friendly
- Documentation is accurate and reflects the current functionality
- Documentation is accessible and well-organized
- All key workflows are documented with examples

Issue #11: Documentation Completion #15

Description

Issue #11: Documentation Completion

Windows (PowerShell as Administrator)

Direct Usage (No Installation)

Basic Usage

Scanning for Malware

Managing Threats

Updating Signature Database

How It Works

Fast Scan

Deep Scan

Security & Privacy

Building from Source

Requirements

Detailed Documentation

License

Acknowledgments

Deep Scan

Quarantine Workflow

Troubleshooting

Common Issues

Database Update Fails

Permission Denied

High False Positive Rate in Deep Scan

Exit Codes

Project Structure

Coding Guidelines

Rust Style

Git Workflow

Testing

Pull Request Process

Code of Conduct

License

Secure Quarantine

Code Analysis

Best Practices

Metadata

Metadata

Assignees

Labels

Projects

Milestone

Relationships

Development

Issue actions