Overwrite an existing directory?

If your goal is to execute a one-line command that:

• Removes and recreates the directory ~/Desktop/foo if it already exists.
• Just creates the directory ~/Desktop/foo if it does not already exist.

Then you can use:

rm -r ~/Desktop/foo; mkdir ~/Desktop/foo

; is equivalent to a newline, but it lets you execute multiple commands on a single line (i.e., as a "single command").

• If the directory you're removing may contain readonly files, you'll need the -f flag to remove them without prompting the user interactively. This is okay, but I do recommend being especially careful with rm -rf .... See man rm for details.
• You need the rm command to finish before the mkdir command executes; this is the reason to use ; instead of &. (A command preceding & runs asynchronously in the background.)
• You need the mkdir command to run when the rm command succeeds; this is the reason to use ; instead of ||.
• You need the mkdir command to run when the rm command fails (usually failure will mean the directory didn't already exist); this is the reason to use ; instead of &&.
• The rm command might fail even when the directory already existed, in which case the mkdir command will fail also, but the error messages will make sense and there's probably no need to add a middle step checking for foo's existence before trying to create it.

See 3.2.3 Lists of Commands in the Bash Reference Manual for more information and explanation about the ;, &, ||, and && operators.

As muru suggested (and Rinzwind elaborated), I do recommend you look into rsync to see if it will meet your backup needs. There are some additional useful guides on the rsync documentation page, as well as this Ubuntu rsync guide.

why mkdir doesn't has this option ?

mkdir creates directories (the "mk" stands for "make"). For it also to recursively delete directories and all the files in them would be bad, because it would violate the principle of least astonishment in a way that would likely lead to data loss.

rmdir doesn't even remove directories that have any (non-directory) files in them. rm has an -r option, which makes sense since rm is expected to remove files (that is its purpose, thus the inherent danger is intuitive and users typically know to be careful when running rm commands).

No, there is no single command to do what you are asking.

Why?

This is the Unix philosophy: Write programs that do one thing and do it well. Write programs to work together.¹

In this instance, the mkdir and rm commands do what you require, and work well together, since rm -r will delete the directory as well, so a subsequent mkdir will create the directory.

¹The Art of Unix Programming, Eric S. Raymond, itself quoting Doug McIlroy.

The command to remove a directory is rm. So you need 2 commands.

rm -r ~/Desktop/foo/
mkdir ~/Desktop/foo/

As shown in comments you can chain them with ; (= do both even if 1st fails) or && (= only mkdir when the rm does not fail).

The -r is for removing dirs. The 1st command also removes ALL contents of the directory. If that is NOT your intention both rm and mkdir are not what you are looking for: permissions are chmod and chown.

why mkdir doesn't has this option ?

Ambiguity. mkdir means make directory. Not remove and make directory. And since the rm command is for deleting stuff there is no need for rmdir to be able to remove a directory.

To do that in the cleanest way I use this:

create_clean_directory(){
    dir_name=$1
    if [ -d "$dir_name" ]; then
        echo "Removing $dir_name"
        rm -rf "$dir_name"
    elif [ -f "$dir_name" ]; then
        echo "File with this name already exists, not a directory."
        exit
    fi
    if mkdir "$dir_name"; then
        echo "Clean directory created: $dir_name"
        return 0
    else
        echo "Creating directory failed: $dir_name"
        return 1
    fi 
}

And to use it:

create_clean_directory <dir_name>

This makes sure that what you are trying to remove is a directory and not a file:

1. -d Check if a directory with that name already exists. if so, delete it.

2. -f Check that no file with this name exists. if so, print error message and exit.

3. Create the new directory and echo success, or if failed, echo failed.