File System Structure

Virtually all modern operating systems have a hierarchical file system.
Assume using a UNIX like system, e.g., linux, OS X.
A directory (or folder) contains other files and/or directories.
The root directory is the starting point of the access. It is denoted by the forward slash character /
At all time, the OS assumes you’re at a specific point in the file system, called your current directory, denoted by the . character.
Double dots .. denotes your parent directory. It is the directory containing your current directory, unless you are at the root of the file system, in which case the parent directory is the root itself.
You can refer to a file or directory by writing its access path either starting from root or from your currect directory. The forward slash character / separates the directories on the path to your target file or directory.
Every user has a home directory. The ~ character denotes your home directory. It is where you are put when you start a terminal session. In general ~user denotes the home directory of user user.

CLI

In a CLI, user interacts with computer by typing in commands on the keyboard, and computer responds by printing out text messages on the user’s monitor (terminal).
Compared to the Graphical User Interface (GUI), a CLI is
- harder to learn
- harder to master
- not as pretty
- faster
- more powerful, in fact, some functionality may not have a GUI equivalent

A shell is a command interpreter. It interprets the commands you type in, executes the commands if possible, prints out the results of execution, or prints out error messages if it can’t execute your commands, or if it encounters any problem.
Some common shells that are in use:
- sh - the Bourne shell
- csh - the C shell
- tcsh - the Tenex C Shell
- ksh - the Korn Shell
- bash - the Bourne-again shell
- zsh - the Z shell

I assume you’ll be using the Bourne-Again Shell (bash) since it is the default shell on the OS X machines in our lab.
The format of a bash simple command is

command [flags] [arguments]

where white spaces (blanks or tabs) separate the components. e.g.

$ ls
$ cp *.txt novel

However, bash is a fullblown scripting language as well as an interpreter. It has regular expressions, conditionals, loops, and functions, e.g.,

$ for f in ch[1-3].ps
  do
        ps2pdf $f 
  done

All commands entered interactively through the keyboard must end in a newline character by the user pressing the enter key.
A valid command is either internal or external. The shell understands an internal command and is able to execute it immediately. Examples of internal commands are

$ pwd
$ alias l=“ls -l”
If the shell does not understand a command, it assumes that it is an external command, and will search all directories as specified in the PATH variable for a file having that command as name. If the file is found and is executable, the shell loads it into memory and executes it. Examples of external commands are

$ ls
$ head file

A text file is meant to be read by humans. It contains characters that can be safely printed to the screen and printers. It doesn’t contain formatting characters or control characters or other binary data.
A text editor is an app that allows the user to conveniently read, write, modify, and save text files. It actually works on buffers in RAM until such time when the user tells it to write those buffers onto secondary storage.
Examples of simple text editors are nano and TextEdit (in plain text mode).
Some editors are meant to be used for writing program source code. They have features useful to programmers. Examples are TextWrangler and Sublime Text.
Some advanced general-purpose text editors have features that are useful for editing all kinds of text files. Examples are emacs and vim.

A process is a program in execution.
A stream is a sequence of bytes.
Every process are allocated 3 standard streams by the OS when it starts:
- standard input - the keyboard
- standard output - the computer screen
- standard error output - the computer screen
The values of these standard streams can easily be changed from the command line by the user

A text file is a kind of text stream so it is reasonable to redirect any of the standard I/O streams to a file.
The command

prog < infile

runs prog with its stardard input coming from infile.
The command

prog > outfile

runs prog with its stardard output redirected to outfile. If outfile does not exist, it will be created with content of the output from prog. If outfile exists, its old content will be overwritten by the output from prog.

The command

prog >> outfile

runs prog with its stardard output redirected to outfile. If outfile does not exist, it will be created with content of the output from prog. If outfile exists, its content will have the output from prog appended to its old content.
The command

prog1 | prog2

has the effect of running both prog1 and prog2 in parallel, but with the stardard output of prog1 being the stardard input of prog2.