Course: From Basic Science to Web Hosting

Module 04 — Linux Fundamentals

What Is the Linux Filesystem?

Difficulty: Beginner → Intermediate
Prerequisites: Lesson 016 — What Really Happens When You Run a Linux Command?
Estimated time: 30–40 minutes

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1. The Big Question

You have already used paths such as:

/storage/websites/templates.cresignsys.com/public

and commands such as:

cd /storage/websites/
ls

But what exactly is this structure?

Why does Linux have:

/etc
/var
/usr
/home
/dev
/proc
/sys

?

To understand Linux administration properly, we first need to understand its filesystem.

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2. What Is a Filesystem?

A filesystem is the software-defined structure used to organize and manage persistent data on storage.

At a simple level:

Storage device
      ↓
Filesystem
      ↓
Directories
      ↓
Files

For example:

SSD
 ↓
Filesystem
 ↓
/
 ├── etc
 ├── var
 ├── home
 └── storage

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3. Linux Has One Main Directory Tree

Linux organizes its filesystem as a tree.

At the top is:

/

This is called:

Root Directory

Do not confuse:

/

with:

root

The first is the filesystem’s top directory.

The second usually refers to the administrative user account.

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4. The Root of the Filesystem

Everything in the normal Linux filesystem hierarchy starts from:

/

For example:

/etc

means:

/
└── etc

And:

/var/log

means:

/
└── var
    └── log

And:

/storage/websites/

means:

/
└── storage
    └── websites

---

5. Absolute Paths

A path beginning with / is an absolute path.

Example:

cd /storage/websites/

It means:

Start from the filesystem root and go to storage, then websites.

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6. Relative Paths

A path without / at the beginning is normally interpreted relative to the current directory.

Suppose:

pwd

returns:

/storage/websites/

Then:

cd templates.cresignsys.com

means:

/storage/websites/templates.cresignsys.com

---

7. pwd

The command:

pwd

means:

Print Working Directory

Example:

pwd

Output:

/storage/websites/templates.cresignsys.com/public

This tells you exactly where you currently are in the filesystem tree.

---

8. ls

The command:

ls

lists directory contents.

For example:

ls

might show:

index.php
wp-config.php
wp-content
wp-admin
wp-includes

---

9. cd

The command:

cd

means:

change directory

Example:

cd /storage/websites/

Then:

pwd

might show:

/storage/websites

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10. The Linux Filesystem Tree

A simplified Linux filesystem might look like:

/
├── bin
├── boot
├── dev
├── etc
├── home
├── lib
├── media
├── mnt
├── opt
├── proc
├── root
├── run
├── sbin
├── srv
├── sys
├── tmp
├── usr
├── var
└── storage

Some modern distributions use merged directories such as /usr/bin being the effective location behind /bin; the exact filesystem layout can vary.

---

11. /bin

Historically:

/bin

contains essential user command binaries.

Examples conceptually include:

ls
cp
mv
cat

On modern Ubuntu systems, /bin is commonly a symbolic link into /usr/bin.

You can inspect it with:

ls -ld /bin

---

12. /sbin

Historically:

/sbin

contains system-administration commands.

Modern Linux distributions may similarly merge this into /usr/sbin.

Examples include tools used for:

System administration
Networking
Disk management
Boot/system maintenance

---

13. /usr

This is one of the most important directories.

It contains a large part of the operating system’s user-space software.

For example:

/usr/bin
/usr/sbin
/usr/lib
/usr/share

Conceptually:

/usr
 ├── bin
 ├── sbin
 ├── lib
 └── share

Many applications and utilities live here.

---

14. /etc

This is extremely important for a server.

/etc

primarily contains system and application configuration.

Examples:

/etc/nginx/
/etc/ssh/
/etc/systemd/
/etc/php/
/etc/mysql/

So when you modify:

/etc/nginx/

you are modifying Nginx configuration.

---

15. Your Nginx Configuration

You have worked with:

/etc/nginx/sites-enabled/

This is part of:

/etc
   ↓
nginx
   ↓
configuration

For example:

/etc/nginx/sites-enabled/templates.cresignsys.com

can contain the Nginx server configuration for that website.

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16. /var

/var is used for variable/changing system data.

Examples:

/var/log
/var/lib
/var/cache

The word “variable” means the contents can change during normal operation.

---

17. /var/log

This directory contains logs.

For example:

/var/log/nginx/

may contain:

access.log
error.log

You can inspect them with:

sudo tail -f /var/log/nginx/error.log

This is extremely useful when troubleshooting websites.

---

18. /var/lib

This is commonly used for persistent application/system state.

For example, databases and system services may maintain data under /var/lib.

The exact location depends on the software.

---

19. /var/cache

This contains cache data maintained by various applications.

Caches can often be regenerated, although you should never assume every file under a cache directory is safe to delete without understanding the specific application.

---

20. /home

This normally contains users’ home directories.

Example:

/home/ubuntu

Inside:

/home/ubuntu/

you may have:

Documents
Downloads
scripts
projects

---

21. /root

This is normally the home directory of the root user:

/root

Remember the distinction:

/
   = filesystem root

root
   = privileged Linux user

and:

/root
   = root user's home directory

These are three related but different concepts.

---

22. /tmp

This directory is commonly used for temporary files.

/tmp

Applications can use it for temporary data.

Important:

Do not assume anything placed in /tmp will persist permanently.

Temporary-directory cleanup behavior depends on the system configuration.

---

23. /boot

This contains files related to booting the operating system.

For example:

/boot

may contain:

Linux kernel
initramfs
bootloader-related files

The exact arrangement depends on the boot architecture.

---

24. /dev

This is a very interesting directory.

/dev

contains device nodes representing devices and device interfaces.

Examples can include:

/dev/null
/dev/zero
/dev/random

and storage/device nodes.

Linux uses the filesystem interface to expose many devices to user-space programs.

---

25. /dev/null

One famous Linux device is:

/dev/null

Anything written to it is discarded.

For example:

echo "hello" > /dev/null

The text disappears.

Conceptually:

Program
 ↓
/dev/null
 ↓
discard

---

26. /dev/zero

Another special device:

/dev/zero

provides a stream of zero-valued bytes when read.

This illustrates an important Linux idea:

Many devices and kernel interfaces can be exposed through file-like interfaces.

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27. /proc

Now we reach something very important.

/proc

is not an ordinary disk directory.

It is a virtual filesystem provided by the kernel.

It exposes information about:

Processes
CPU
Memory
Kernel state
System information

For example:

cat /proc/cpuinfo

can display processor information.

---

28. /proc/meminfo

Try:

cat /proc/meminfo

You can see information about memory.

Conceptually:

Linux kernel
      ↓
/proc
      ↓
Information exposed to user space

The data is dynamically generated by the kernel.

---

29. /proc/PID

Every process has a process ID, commonly called:

PID

Suppose a process has:

PID = 1234

Linux can expose information under:

/proc/1234/

Conceptually:

Process
  ↓
PID
  ↓
/proc/PID

This becomes extremely useful when learning process management.

---

30. /sys

Similar to /proc, Linux provides:

/sys

which is a virtual filesystem exposing information about devices, drivers, buses, and kernel device models.

Conceptually:

Hardware
   ↓
Kernel device model
   ↓
/sys
   ↓
User-space tools

---

31. /run

/run

contains runtime state.

It is generally temporary and is usually populated during boot.

Examples can include:

PID information
Sockets
Runtime service state

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32. /media

This is commonly used as a location for automatically mounted removable media.

For example:

/media/username/USB

---

33. /mnt

Traditionally used as a temporary or manually managed mount point.

For example:

/mnt/data

could be used for a mounted filesystem.

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34. /opt

/opt

is commonly used for optional/add-on application software.

For example, some third-party software may install under:

/opt/application/

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35. /srv

/srv

is intended for data served by the system.

For example, a service could theoretically use:

/srv/www/

However, server administrators often choose other directory structures based on their architecture.

Your:

/storage/websites/

is perfectly valid as a custom hosting layout.

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36. /storage

This is important for your setup.

Unlike directories such as /etc or /var, /storage is not a mandatory standard Linux directory.

You or your hosting architecture created it for your own purpose.

For example:

/storage
   └── websites
       ├── site1
       ├── site2
       └── site3

This is a good example of Linux’s flexibility.

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37. Your Hosting Structure

Your architecture can be represented as:

/
└── storage
    └── websites
        └── templates.cresignsys.com
            └── public
                ├── index.php
                ├── wp-admin
                ├── wp-content
                ├── wp-includes
                └── wp-config.php

This is the physical filesystem organization of the website files.

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38. Filesystem vs Website URL

This distinction is extremely important.

Your filesystem path might be:

/storage/websites/templates.cresignsys.com/public/

But the user sees:

https://templates.cresignsys.com/

These are not the same thing.

Nginx creates the connection between them.

Conceptually:

Browser URL
     ↓
Nginx configuration
     ↓
Filesystem path

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39. Nginx root

A typical Nginx configuration might contain something conceptually like:

server {
    server_name templates.cresignsys.com;

    root /storage/websites/templates.cresignsys.com/public;
}

This tells Nginx:

Use this filesystem directory as the document root for this virtual host.

Therefore:

https://templates.cresignsys.com/

can map to:

/storage/websites/templates.cresignsys.com/public/

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40. One URL Request

Suppose someone requests:

https://templates.cresignsys.com/about.html

Conceptually:

Browser
 ↓
DNS
 ↓
Server IP
 ↓
TCP 443
 ↓
TLS
 ↓
Nginx
 ↓
server_name
 ↓
root directory
 ↓
about.html

The physical file might be:

/storage/websites/templates.cresignsys.com/public/about.html

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41. Why /etc and /storage Are Different

This distinction will become extremely useful.

/etc
 ↓
Configuration

while:

/storage
 ↓
Your website data

For example:

/etc/nginx/

contains instructions telling Nginx how to serve the site.

While:

/storage/websites/templates.cresignsys.com/public/

contains the website itself.

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42. Configuration vs Data

This is a general systems principle:

Configuration
      ↓
How the software should behave

Data
      ↓
What the software works with

For your website:

Nginx configuration
      ↓
How requests are handled

WordPress files/database
      ↓
Website content

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43. Logs Are Another Layer

Nginx also produces logs:

/var/log/nginx/

So we have:

/etc/nginx/
     ↓
Configuration

/storage/websites/
     ↓
Website data

/var/log/nginx/
     ↓
Operational records

These three locations have completely different purposes.

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44. A Practical Example

Suppose the website gives:

502 Bad Gateway

Don’t immediately edit WordPress.

First consider:

Nginx
 ↓
PHP-FPM

Check:

sudo systemctl status nginx

Then:

sudo systemctl status php*-fpm

And inspect:

sudo tail -f /var/log/nginx/error.log

Now you are troubleshooting according to the architecture.

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45. Another Example: 404

Suppose:

https://templates.cresignsys.com/test.html

returns:

404 Not Found

Possible causes include:

Wrong Nginx root
Wrong URL
File does not exist
Nginx location rule
WordPress routing

First understand which layer is responsible.

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46. Filesystem Hierarchy to Remember

For your web-hosting work, memorize these first:

/
├── etc       → configuration
├── var       → changing data/logs
├── usr       → installed user-space software
├── home      → user home directories
├── root      → root user's home
├── tmp       → temporary data
├── dev       → device interfaces
├── proc      → kernel/process information
├── sys       → kernel/device information
├── run       → runtime state
└── storage   → your custom hosting storage

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47. The Deeper Architecture

Now connect today’s lesson with everything before it:

HARDWARE
   ↓
CPU / RAM / SSD
   ↓
Linux Kernel
   ↓
Virtual Filesystem Interface
   ↓
Filesystem
   ↓
Directories
   ↓
Configuration / Data / Logs
   ↓
Applications

And for your hosting server:

Linux
 │
 ├── /etc/nginx
 │       ↓
 │   Nginx configuration
 │
 ├── /var/log/nginx
 │       ↓
 │   Nginx logs
 │
 └── /storage/websites
         ↓
     Website files

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48. Most Important Concept

Don’t memorize directories as a random list.

Understand their purpose:

/etc
  = "How should the system/software behave?"

/var
  = "What changing operational data exists?"

/usr
  = "What software is installed?"

/home
  = "Where are user files?"

/dev
  = "How does user space interact with devices?"

/proc
  = "What does the kernel expose about processes/system?"

/sys
  = "What does the kernel expose about devices/system structure?"

/storage
  = "Where did we choose to keep our hosting data?"

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49. Quick Check

What is /?

The root of the Linux filesystem hierarchy.

What is /etc?

Primarily system and application configuration.

What is /var/log?

A common location for system/application logs.

What is /usr?

A major hierarchy containing user-space programs, libraries, and shared data.

What is /proc?

A kernel-provided virtual filesystem exposing process and system information.

What is /sys?

A kernel-provided virtual filesystem exposing device/kernel information.

What is /storage?

In your server, a custom directory used for hosting data.

Where are your website files?

For example:

/storage/websites/templates.cresignsys.com/public/

Where is Nginx configuration?

Commonly under:

/etc/nginx/

Where are Nginx logs?

Commonly:

/var/log/nginx/

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Next Lesson — 018

Linux Users, Groups, Ownership and Permissions

This is the next essential foundation before managing multiple websites.

We will build from the deepest basics:

User
 ↓
Group
 ↓
Process identity
 ↓
File owner
 ↓
Permissions
 ↓
r / w / x
 ↓
chmod
 ↓
chown
 ↓
chgrp
 ↓
sudo
 ↓
www-data
 ↓
Nginx
 ↓
PHP-FPM
 ↓
WordPress

Then we will answer an important real-world question:

Why can Nginx/PHP sometimes read a WordPress file but cannot write to it?

That leads directly into secure multi-domain web hosting.