Scaffolding and Directory Structures

I'm glad you asked. (I was going to talk about it anyway.) Each Drupal installation from Drupal 6 onwards has the same file structure, files & infrastructure.

This means work which should be quickly and easily predictable and repeatable via scripting (through Drush, Gulp, or Grunt, for example) and version control (such as Git).

No matter which version of Drupal you might be using, your directory will look something like this:

# Drupal-6.x-dev (2016-April)

includes/
misc/
modules/
profiles/
scripts/
sites/
themes/
.htaccess
CHANGELOG
COPYRIGHT
cron.php
index.php
install.php
INSTALL.txt
INSTALL.mysql.txt
INSTALL.pgsql.txt
LICENSE.txt
MAINTAINERS.txt
robots.txt
upgrade.php
UPGRADE.txt
xmlrpc.php

Advanced users, being quite smarmy and up with the hip provisioning, might even have something like this:

# Drupal-7.x-dev (2016-April)

includes/
misc/
modules/
profiles/
scripts/
sites/
themes/
.htaccess
authorize.php
CHANGELOG
COPYRIGHT
cron.php
index.php
install.php
INSTALL.txt
INSTALL.mysql.txt
INSTALL.pgsql.txt
INSTALL.sqlite.txt
LICENSE.txt
MAINTAINERS.txt
README.txt
robots.txt
upgrade.php
UPGRADE.txt
web.xml
xmlrpc.php

and people way over your head (and someimtes mine) have something like this:

# Drupal-8.4.x-dev (2017-Oct) https://github.com/drupal/drupal

core/
modules/
profiles/
sites/
themes/
vendors/
.csslintrc
.editorconfig
.eslintignore
.eslintrc.json
.gitattributes
.htaccess
README.txt
autoload.php
composer.json
composer.lock
example.gitignore
index.php
robots.txt
update.php
web.config

Notice the similarities? From Drupal 6 to Drupal 7, the file structure barely changed at all.

In Drupal 8 it got to be awesome because the reversed the setup and moved all of the Drupal Core files into the core/ folder. Instead of being locked only within the sites/ folder for changes and Development, Site Owners instead get to make all of their changes in the folders outside of the core/ folder.

To reiterate, Dont' Hack Core

The sites/ and profiles/ folders are maintained through all installations. In Drupal 6 and Drupal 7, all Development work happens within either of these two folders. In Drupal 8, as I mentioned, custom/contrib work is done outside of the core/ folder.

Drupal 7 Directory Structure

When using standardized Drupal 7 Best Practices, the sites/ folder will generally have the same directory structure between installations as well, such as:

all/
  - files/
  - modules/
    - contrib/
    - custom/
  - themes/
default/
  - files/
  - modules/ (This should only be used when using Drupal Multisite)
  - themes/ (This should only be used when using Drupal Multisite)
  - default.settings.php
  - settings.php
  - local-settings.php

Note - Your installation may not have a local-settings.php file, but you should before moving into production. We can get into that later.

Drupal 8 Directory Stucture

Drupal 8 adopted Composer in a very heavy way, so you'll want to get used to seeing Composer everywhere in Drupal. Everywhere.

In addition, we've seen a very heavy upshoot in Composer integrations using 'Continuous Integration', to keep codebases itty-bitty-tiny for the fastest deployments.

core/
drush/
modules/
  - files/
  - modules/
    - contrib/
    - custom/
  - themes/
sites/
  default/
    - files/    
    - default.settings.php
    - settings.php
    - local.settings.php

Note - In Drupal 8, it does not really give SIte Builders a *choice in using local.settings.php, even including content within settings.php by default to support it.