In Debian-based systems, Apache2 uses a logical separation between available configurations and active configurations through two directories:

/etc/apache2/sites-available/  # Stores all possible site configurations
/etc/apache2/sites-enabled/     # Contains symlinks to enabled configurations

The sites-available directory serves as a repository for all virtual host configurations, whether active or not. The sites-enabled directory contains symbolic links to configuration files that should be active.

When Apache starts, it only reads configurations from sites-enabled. The standard practice is to create symlinks from sites-enabled to sites-available:

# Enable a site
sudo a2ensite example.com.conf

# Disable a site  
sudo a2dissite example.com.conf

Here's what happens when you create a new virtual host:

# 1. Create config in sites-available
sudo nano /etc/apache2/sites-available/example.com.conf

# 2. Enable it
sudo a2ensite example.com.conf

# 3. Verify symlink
ls -l /etc/apache2/sites-enabled/example.com.conf
# Should show: example.com.conf -> ../sites-available/example.com.conf

This architecture provides several benefits:

• Easy to disable sites without deleting configuration files
• Clean organization of all possible configurations
• Simple backup of all potential configurations
• Standardized across Debian-based systems

1. Editing the symlink: Always edit files in sites-available, not sites-enabled.

2. Missing symlinks: If Apache isn't loading your config, verify the symlink exists.

3. File naming: Ensure your config files end with .conf for proper recognition.

In Debian-based systems with Apache2, you'll find this structure:

/etc/apache2/

├── sites-available/

│   ├── 000-default.conf

│   ├── example.com.conf

├── sites-enabled/

│   ├── 000-default.conf -> ../sites-available/000-default.conf

│   ├── example.com.conf -> ../sites-available/example.com.conf
The key differences:
sites-available/ - Stores all possible virtual host configurations

sites-enabled/ - Contains symlinks to active configurations
Apache only reads files from sites-enabled. The identical content you observed occurs because:
ls -l /etc/apache2/sites-enabled
Shows they're symbolic links pointing back to sites-available.
Enable a site:

sudo a2ensite example.com.conf
Disable a site:

sudo a2dissite example.com.conf
Here's a sample configuration in sites-available:


<VirtualHost *:80>

    ServerName example.com

    ServerAlias www.example.com

    DocumentRoot /var/www/example.com

    ErrorLog ${APACHE_LOG_DIR}/error.log

    CustomLog ${APACHE_LOG_DIR}/access.log combined

</VirtualHost>


Advantages:

- Easy to disable sites without deleting configs

- Clean separation between available and active configs

- Atomic changes (modify in available, then enable)

- Supports version control of all possible configs
Create custom site templates:
sudo cp /etc/apache2/sites-available/000-default.conf /etc/apache2/sites-available/template.conf
Then modify as needed for new sites.
Common issues:

- Broken symlinks in sites-enabled

- Syntax errors in available configs

- Permission problems

- Missing a2ensite/a2dissite commands
Check with:

apache2ctl configtest