The Filesystem Hierarchy

Linux has no drive letters: there is one tree rooted at /, and every disk appears inside it at a mount point. The layout follows the Filesystem Hierarchy Standard 3.0 (2015), closely enough that you can guess right on an unfamiliar server.

The parts of the filesystem hierarchy a web developer meets
Directory	Holds	You use it for
/etc	Host configuration	Apache 129 , PHP, MySQL 524 , cron
/var/www	Served content	Your document root
/var/log	Log files	Debugging failed requests
/var/lib	Application state	The MySQL data directory
/run	Runtime data, cleared at boot	PID files, Unix sockets
/home, /root	Home directories	Your account, SSH keys
/usr/bin, /usr/sbin	Programs	php, mysql, apache2ctl
/tmp	World-writable scratch	Uploads in flight, sessions

/bin, /sbin and /lib are now symbolic links into /usr (the "/usr merge"), so /bin/bash and /usr/bin/bash are one file. And a service started with PrivateTmp=yes gets its own /tmp, which is why a file PHP wrote there can be invisible from your shell (Overrides and Sandboxing).

Where the stack actually lives

Debian 319 and Ubuntu 225 split Apache's configuration into small files enabled by symlink with a2enmod and a2ensite, and call everything apache2. Red Hat systems keep one httpd.conf plus conf.d fragments and call everything httpd.

Where Apache, PHP and MySQL put their files on the two distribution families
Component	Debian and Ubuntu	RHEL 664 , Rocky, AlmaLinux 7,122 , Fedora 1,480
Package and service	apache2	httpd
Main Apache config	/etc/apache2/apache2.conf	/etc/httpd/conf/httpd.conf
Virtual hosts	/etc/apache2/sites-available/	/etc/httpd/conf.d/*.conf
Modules	mods-available plus a2enmod	/etc/httpd/conf.modules.d/
Error log	/var/log/apache2/error.log	/var/log/httpd/error_log
Apache runs as	www-data	apache
php.ini	/etc/php/8.5/<sapi>/php.ini	/etc/php.ini
PHP-FPM pool	/etc/php/8.5/fpm/pool.d/www.conf	/etc/php-fpm.d/www.conf
MySQL config	/etc/mysql/my.cnf	/etc/my.cnf, /etc/my.cnf.d/

Note the underscore in Red Hat's error_log: a tail copied from the wrong tutorial fails with "No such file or directory". PHP differs most. Debian gives every SAPI (cli, fpm, apache2) its own php.ini, so raising memory_limit for the command line does nothing for the web server. Ask each program.

Asking each service where its own configuration livesShell

php --ini | head -n 3                                 # the CLI's php.ini
php-fpm8.5 -i | grep 'Loaded Configuration'           # the web server's php.ini
apache2ctl -V | grep -E 'HTTPD_ROOT|SERVER_CONFIG'    # on RHEL: httpd -V
mysqld --verbose --help | grep -A1 'Default options'  # my.cnf search order

Output

Configuration File (php.ini) Path: "/etc/php/8.5/cli"
Loaded Configuration File:         "/etc/php/8.5/cli/php.ini"
Scan for additional .ini files in: "/etc/php/8.5/cli/conf.d"
Loaded Configuration File => /etc/php/8.5/fpm/php.ini
 -D HTTPD_ROOT="/etc/apache2"
 -D SERVER_CONFIG_FILE="apache2.conf"
Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf ~/.my.cnf

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Where the stack actually lives