# Server Toolkit - Project Structure

## Directory Layout

```
server-toolkit/
├── launcher.sh              # Main entry point
├── README.md                # Project documentation
├── TROUBLESHOOTING.md       # Troubleshooting guide
├── AUDIT-REPORT.md          # Project audit results
├── REFDB_FORMAT.txt         # Development notes & bug tracker
│
├── config/                  # Configuration files
│   ├── settings.conf        # Main configuration
│   ├── settings.conf.minimal # Minimal config (template)
│   ├── whitelist-ips.txt    # IP whitelist for bot analyzer
│   └── whitelist-user-agents.txt  # User-agent whitelist
│
├── lib/                     # Core libraries
│   ├── common-functions.sh  # Shared utilities (print, colors, etc.)
│   ├── system-detect.sh     # Auto-detect control panel, OS, etc.
│   ├── user-manager.sh      # User/domain selection functions
│   ├── reference-db.sh      # System reference database builder
│   └── mysql-analyzer.sh    # MySQL analysis functions
│
├── modules/                 # Feature modules
│   ├── security/
│   │   └── bot-analyzer.sh  # ✓ Bot & botnet analysis (WORKING)
│   ├── performance/
│   │   └── mysql-query-analyzer.sh  # ✓ MySQL query analysis (WORKING)
│   ├── wordpress/           # (Empty - future development)
│   ├── backup/              # (Empty - future development)
│   ├── monitoring/          # (Empty - future development)
│   ├── troubleshooting/     # (Empty - future development)
│   └── reporting/           # (Empty - future development)
│
└── tools/                   # Diagnostic & testing tools
    ├── diagnostic-report.sh # System diagnostic collector
    └── test-domain-detection.sh  # Domain detection validator
```

## File Purposes

### Root Level
- **launcher.sh** - Main menu system, calls modules
- **README.md** - User-facing documentation
- **TROUBLESHOOTING.md** - Help guide for common issues
- **AUDIT-REPORT.md** - Technical audit results (for developers)
- **REFDB_FORMAT.txt** - Development log, bug tracking, enhancement notes

### Config Directory
Contains user-configurable settings:
- **settings.conf** - Main config (includes unused future settings)
- **settings.conf.minimal** - Clean template with only current settings
- **whitelist-*.txt** - Bot analyzer whitelists

### Lib Directory
Core library functions sourced by modules:
- **common-functions.sh** - Colors, print functions, formatting
- **system-detect.sh** - Auto-detect environment (cPanel/Plesk/etc)
- **user-manager.sh** - User selection, domain detection
- **reference-db.sh** - Build/manage system reference database
- **mysql-analyzer.sh** - MySQL analysis helper functions

### Modules Directory
Feature implementations:
- **security/** - Security tools (bot analyzer, etc.)
- **performance/** - Performance tools (MySQL analyzer, etc.)
- **wordpress/** through **reporting/** - Placeholder for future

### Tools Directory
Diagnostic and testing utilities:
- **diagnostic-report.sh** - Generates comprehensive system report
- **test-domain-detection.sh** - Quick validation of domain detection

## Working Features

### Fully Implemented (✓)
1. **Bot & Botnet Analyzer** (`modules/security/bot-analyzer.sh`)
   - Comprehensive log analysis
   - Threat scoring
   - IP blocking recommendations
   - CSF integration
   - Attack vector detection

2. **MySQL Query Analyzer** (`modules/performance/mysql-query-analyzer.sh`)
   - Slow query detection
   - Query performance analysis

3. **System Detection** (`lib/system-detect.sh`)
   - Auto-detect: cPanel, Plesk, InterWorx
   - OS, web server, database detection
   - Resource monitoring

4. **User Management** (`lib/user-manager.sh`)
   - Interactive user selection
   - Arrow-key navigation
   - Search with confirmation
   - Domain detection

## In Development (Future)

- WordPress Management (11 planned scripts)
- Backup & Recovery (7 planned scripts)
- Monitoring & Alerts (5 planned scripts)
- Troubleshooting (9 planned scripts)
- Reporting (6 planned scripts)

See AUDIT-REPORT.md for complete list.

## Configuration

Most settings auto-detect on first run. Manual configuration available in:
- `config/settings.conf` - All settings (includes future features)
- `config/settings.conf.minimal` - Only current features

## Logs & Cache

Runtime files (auto-created):
- `.sysref` - System reference database cache
- `/tmp/bot_analysis_*.txt` - Bot analysis reports
- `/tmp/mysql_analysis_*.txt` - MySQL analysis reports
- `/tmp/server-toolkit-*` - Temporary session directories

## For Developers

Key technical documentation:
- **AUDIT-REPORT.md** - What's implemented vs. planned
- **REFDB_FORMAT.txt** - Bug fixes, enhancements, lessons learned
- **TROUBLESHOOTING.md** - Common issues and debug procedures