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Clean BOM Senior 🧹✨

A production-ready shell utility for safely removing invisible UTF-8 BOM and Windows CRLF from source code files

Clean BOM Senior is a robust, enterprise-grade bash script designed to detect and remove invisible UTF-8 Byte Order Marks (BOM) and Windows CRLF line endings that can cause critical errors in PHP, JavaScript, CSS, and other source code files.

⚡ Quick Start

# Clone and install
git clone https://github.com/paulmann/Clean_BOM_Senior.git
cd Clean_BOM_Senior
chmod +x clean-bom-senior.sh

# Clean all files recursively
./clean-bom-senior.sh

# Preview what would be cleaned (dry run)
./clean-bom-senior.sh --dry-run

# Verbose mode with detailed logging
./clean-bom-senior.sh --verbose

# Clean specific files
./clean-bom-senior.sh file1.php file2.js config.xml

# Disable BOM removal (only normalize CRLF)
./clean-bom-senior.sh --no-bom-clear

# Disable CRLF normalization (only remove BOM signatures)
./clean-bom-senior.sh --no-rn-normalize

# Preview with selective cleaning actions
./clean-bom-senior.sh --dry-run --no-bom-clear --verbose

📋 Table of Contents

🚨 Why Clean BOM Senior?
- The Hidden Problem
- Real-World Impact
✨ Key Features
📋 Installation & Usage
🏗️ Advanced Features
🔗 DevOps Integration
🏢 Team & Enterprise Usage
🔍 Troubleshooting
🤝 Contributing
📄 License
👨‍💻 Author & Support
- Getting Help
- Related Projects
🎯 Roadmap
- Upcoming Features
- Version History

🚨 Why Clean BOM Senior?

The Hidden Problem

UTF-8 BOM markers are invisible 3-byte sequences (EF BB BF) that can break your code:

<?php
// ⚠️ This file has invisible BOM - will cause FATAL ERROR!
namespace MyApp\Controllers;  // Fatal error: Namespace declaration statement has to be...

// ⚠️ BOM here causes encoding issues
import { Component } from 'react';  // Potential parsing errors

Real-World Impact

PHP Fatal Errors: BOM before namespace or declare(strict_types=1) statements
JavaScript Parsing Issues: BOM can break module imports and cause encoding problems
CSS Rendering Problems: BOM may cause unexpected styling behavior
Cross-Platform Conflicts: Mixed CRLF/LF line endings between Windows and Unix systems
CI/CD Pipeline Failures: Automated builds failing due to encoding issues

✨ Key Features

🛡️ Enterprise-Grade Safety

Atomic Operations: Changes are applied atomically or rolled back completely
Automatic Backups: Creates backup copies during processing with automatic cleanup
File Integrity: Preserves original file ownership, permissions, and timestamps
Error Recovery: Comprehensive rollback mechanism on any failure

🎯 Intelligent Processing

Smart Detection: Only processes files that actually contain BOM or CRLF issues
Multi-Format Support: PHP, CSS, JS, TXT, XML, HTM, HTML files
Size Limits: Built-in protection against processing oversized files (100MB default)
Extension Filtering: Configurable file extension support

📊 Comprehensive Reporting

Detailed Statistics: Complete breakdown of processed files by type and issues fixed
Progress Tracking: Real-time logging with timestamps and color coding
Dry-Run Mode: Preview operations without making changes
Error Classification: Categorized error reporting with resolution suggestions

🔄 DevOps Integration

CI/CD Ready: Perfect for integration into build pipelines
Git Hooks: Ideal for pre-commit hooks and automated workflows
Cross-Platform: Works on Linux, macOS, and Unix systems
No Dependencies: Pure bash script with standard Unix utilities only

📋 Installation & Usage

System Requirements

Shell: Bash 4.0+ (or compatible: sh, dash)
OS: Linux, macOS, Unix-like systems
Tools: Standard utilities (find, sed, od, grep, stat, mv, cp, touch, chown, chmod)
Permissions: Write access to target directory and temp folder

Installation Options

Option 1: Direct Download

wget https://github.com/paulmann/Clean_BOM_Senior/raw/main/clean-bom-senior.sh
chmod +x clean-bom-senior.sh
./clean-bom-senior.sh --help

Option 2: Git Clone

git clone https://github.com/paulmann/Clean_BOM_Senior.git
cd Clean_BOM_Senior
chmod +x clean-bom-senior.sh

Option 3: Global Installation

# Install globally (requires sudo)
sudo curl -o /usr/local/bin/bom https://github.com/paulmann/Clean_BOM_Senior/raw/main/clean-bom-senior.sh
sudo chmod +x /usr/local/bin/bom

# Now use anywhere with simple command
bom --help
bom --dry-run

Option 4: User Alias

# Add to ~/.bashrc or ~/.bash_profile
alias bom='/path/to/clean-bom-senior.sh'

# Reload shell configuration
source ~/.bashrc

# Use the alias
bom --verbose

Command-Line Options

Option	Description
`-h, --help`	Show help message and exit
`-v, --verbose`	Enable detailed output
`-n, --dry-run`	Preview mode: show what would change
`-V, --version`	Show script version info
`--no-bom-clear`	NEW: Do not remove BOM
`--no-rn-normalize`	NEW: Do not normalize CRLF (`\r\n`) lines

Usage Examples

Basic Usage

# Clean all supported files in current directory and subdirectories
./clean-bom-senior.sh

# Clean with verbose output
./clean-bom-senior.sh --verbose

# Preview changes without modifying files
./clean-bom-senior.sh --dry-run

# Disable BOM removal (keep BOM, fix CRLF)
./clean-bom-senior.sh --no-bom-clear

# Disable CRLF normalization (keep CRLF, remove BOM)
./clean-bom-senior.sh --no-rn-normalize

# Both options
./clean-bom-senior.sh --no-bom-clear --no-rn-normalize

# Dry run shows what "would" (or "would not") be done under current flags
./clean-bom-senior.sh --dry-run --no-bom-clear

Specific Files

# Clean specific files
./clean-bom-senior.sh config.php script.js style.css

# Clean files with verbose logging
./clean-bom-senior.sh --verbose src/Controller.php src/Model.php

# Preview specific files
./clean-bom-senior.sh --dry-run templates/*.php

Directory Processing

# Clean entire project (recursive)
./clean-bom-senior.sh

# Clean specific directory with verbose output
./clean-bom-senior.sh --verbose src/

# Preview entire project changes
./clean-bom-senior.sh --dry-run --verbose

🏗️ Advanced Features

File Preservation Guarantees

Clean BOM Senior ensures complete file integrity:

# Before processing (example file attributes)
-rw-r--r-- 1 developer team 1234 Oct 28 10:30 script.php

# After processing - ALL attributes preserved
-rw-r--r-- 1 developer team 1156 Oct 28 10:30 script.php
# ✅ Same owner, group, permissions, timestamp
# ❌ Only file size changed (BOM removed: 1234 → 1156 bytes)

What's Preserved:

✅ Ownership: Original user and group ownership
✅ Permissions: File mode/access rights (755, 644, etc.)
✅ Timestamps: Last modified time (crucial for build systems)
✅ Content Integrity: Only BOM and CRLF are removed

Comprehensive Statistics

# Example output with statistics
=== PROCESSING SUMMARY ===
Execution time: 2 seconds
Files processed: 15
Files skipped (clean): 8
Errors encountered: 0

--- Issues Fixed ---
BOM signatures removed: 12
CRLF line endings fixed: 8

--- File Type Distribution ---
.php files: 10
.js files: 3
.css files: 2

Supported File Types

Extension	Purpose	Common Issues
`.php`	PHP scripts	BOM breaks `namespace`, `declare()`
`.css`	Stylesheets	BOM can affect rendering
`.js`	JavaScript	BOM may break modules/imports
`.txt`	Text files	Mixed line endings
`.xml`	XML documents	BOM affects XML parsing
`.sh`	XML documents	BOM affects XML parsing
`.htm/.html`	Web pages	Encoding display issues

Error Handling

Clean BOM Senior provides bulletproof error handling:

--- Error Breakdown ---
Access errors: 2        # Permission denied files
File size errors: 1     # Files exceeding size limit
Processing errors: 0    # Content processing failures
Other errors: 0         # Miscellaneous issues

Error Recovery Features:

🔄 Automatic Rollback: Failed operations are completely reverted
💾 Backup & Restore: Temporary backups ensure data safety
📝 Detailed Logging: Every error includes context and suggestions
🛡️ Safe Defaults: Conservative approach prevents data loss

🔗 DevOps Integration

CI/CD Pipeline Integration

GitHub Actions

name: Clean BOM
on: [push, pull_request]
jobs:
  clean-bom:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Clean BOM markers
        run: |
          wget https://github.com/paulmann/Clean_BOM_Senior/raw/main/clean-bom-senior.sh
          chmod +x clean-bom-senior.sh
          ./clean-bom-senior.sh --dry-run --verbose

GitLab CI

clean_bom:
  stage: test
  script:
    - wget https://github.com/paulmann/Clean_BOM_Senior/raw/main/clean-bom-senior.sh
    - chmod +x clean-bom-senior.sh
    - ./clean-bom-senior.sh --verbose
  only:
    - merge_requests
    - main

Git Hooks

Pre-commit Hook

#!/bin/bash
# .git/hooks/pre-commit
./tools/clean-bom-senior.sh --dry-run > /dev/null
if [ $? -ne 0 ]; then
    echo "❌ BOM or CRLF issues found. Run: ./tools/clean-bom-senior.sh"
    exit 1
fi
echo "✅ No BOM/CRLF issues detected"

Pre-push Hook

#!/bin/bash
# .git/hooks/pre-push
echo "🧹 Cleaning BOM markers before push..."
./tools/clean-bom-senior.sh --verbose

Docker Integration

# Dockerfile example
FROM php:8.1-alpine
COPY . /app
WORKDIR /app

# Clean BOM as part of build process
RUN wget https://github.com/paulmann/Clean_BOM_Senior/raw/main/clean-bom-senior.sh \
    && chmod +x clean-bom-senior.sh \
    && ./clean-bom-senior.sh \
    && rm clean-bom-senior.sh

CMD ["php", "index.php"]

🏢 Team & Enterprise Usage

Project Setup

# Add to project tools
mkdir -p tools
cd tools
wget https://github.com/paulmann/Clean_BOM_Senior/raw/main/clean-bom-senior.sh
chmod +x clean-bom-senior.sh

# Create project alias in package.json (for Node.js projects)
{
  "scripts": {
    "clean-bom": "./tools/clean-bom-senior.sh --verbose",
    "check-bom": "./tools/clean-bom-senior.sh --dry-run"
  }
}

# Or in Makefile
clean-bom:
	./tools/clean-bom-senior.sh --verbose

check-bom:
	./tools/clean-bom-senior.sh --dry-run

Team Workflow

# Before committing changes
npm run check-bom          # or: make check-bom
# If issues found:
npm run clean-bom          # or: make clean-bom

# Regular maintenance
./tools/clean-bom-senior.sh --verbose  # Weekly cleanup

IDE Integration

VS Code Task (`.vscode/tasks.json`)

{
    "version": "2.0.0",
    "tasks": [
        {
            "label": "Clean BOM",
            "type": "shell",
            "command": "./tools/clean-bom-senior.sh",
            "args": ["--verbose"],
            "group": "build",
            "presentation": {
                "echo": true,
                "reveal": "always"
            }
        }
    ]
}

🔍 Troubleshooting

Common Issues

Permission Errors

# Problem: Cannot write to file
[ERROR] Cannot write to file: protected.php

# Solution: Check file permissions
chmod 644 protected.php
# Or run with appropriate permissions
sudo ./clean-bom-senior.sh

No Files Found

# Problem: "No files found with supported extensions"
# Solution: Verify you're in the correct directory
ls -la *.{php,css,js,html}  # Check for supported files
pwd                          # Verify current directory

Large Files Skipped

# Problem: File size exceeds limit
# Check file sizes
find . -name "*.php" -size +100M -exec ls -lh {} \;

# Solution: Process large files individually if needed
./clean-bom-senior.sh specific-large-file.php

Debugging Commands

# Check for BOM manually
hexdump -C file.php | head -1
# Look for: EF BB BF at beginning

# Check for CRLF
od -c file.php | head -5
# Look for: \r \n sequences

# Verify UTF-8 encoding
file -i file.php
# Should show: charset=utf-8

Recovery Procedures

# If something goes wrong, backups are created as:
# filename.bak.PROCESS_ID

# Restore from backup
cp file.php.bak.12345 file.php

# Clean up backup files
rm *.bak.*

🤝 Contributing

We welcome contributions! Here's how to get involved:

Development Setup

git clone https://github.com/paulmann/Clean_BOM_Senior.git
cd Clean_BOM_Senior

# Run tests (if available)
./test-suite.sh

# Check script syntax
bash -n clean-bom-senior.sh

# Test dry run
./clean-bom-senior.sh --dry-run --verbose

Contribution Guidelines

Fork the repository
Create a feature branch (git checkout -b feature/amazing-feature)
Test your changes thoroughly
Commit your changes (git commit -m 'Add amazing feature')
Push to the branch (git push origin feature/amazing-feature)
Open a Pull Request

Code Standards

✅ POSIX Compliance: Ensure compatibility across different shells
✅ Error Handling: Comprehensive error checking and recovery
✅ Documentation: Comment complex logic and functions
✅ Testing: Verify functionality across different file types
✅ Backwards Compatibility: Maintain compatibility with existing usage

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

MIT License

Copyright (c) 2025 Mikhail Deynekin

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

👨‍💻 Author & Support

Mikhail Deynekin

🌐 Website: deynekin.com
📧 Email: [email protected]
🐙 GitHub: @paulmann

Getting Help

📖 Documentation: Read this README thoroughly
🐛 Bug Reports: Open an issue
💡 Feature Requests: Request features
💬 Questions: Check Discussions

Related Projects

ssg/unbom - .NET tool for BOM removal
stdlib-js/string-remove-utf8-bom - Node.js BOM removal

🎯 Roadmap

Upcoming Features

Web Interface: Browser-based file upload and cleaning
Docker Image: Pre-built container for CI/CD integration
Windows Support: Native Windows PowerShell version
Plugin System: Extensible architecture for custom processors
Performance Optimization: Parallel processing for large codebases
Advanced Reporting: HTML/JSON output formats

Version History

v2.07.0 (2025-09-30):
- Added --no-bom-clear and --no-rn-normalize CLI flags for selective disabling of BOM and CRLF operations
- Fixed variable leakage in while read loops (uses process substitution consistently)
- Enhanced dry-run output to reflect disabled operations
- Improved argument parsing and help text
- Minor refactoring for code clarity/maintainability
v2.06.4 (2025-09-28): Fixed statistics reporting, improved process substitution
v2.06.3 (2025-09-28): Resolved unbound variable issues, enhanced error handling
v2.06.2 (2025-09-28): Added file attribute preservation, global command support
v2.05.0 (2025-09-28): Major refactor with comprehensive statistics and CI/CD integration

⭐ Star this repository if it helped you!

Clean BOM Senior - Making source code clean, one file at a time 🧹✨

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