Files

Comparable to files as you see them in the file system. 

Folders

Comparable to directories on a file system.  In the Workbench, folders are contained in projects or other folders. Folders can contain files and other folders.

Projects

Contain folders and files. Projects are used for builds, version management, sharing, and resource organization. Like folders, projects map to directories in the file system. (When you create a project, you specify a location for it in the file system.)

A project is either open or closed. When a project is closed, it cannot be changed in the Workbench.  The resources of a closed project will not appear in the Workbench, but the resources still reside on the local file system.  Closed projects require less memory.  Since they are not examined during builds, closing a project can improve build time.

When a project is open, the structure of the project can be changed and you will see the contents. 

Folders and files directly below projects can be linked to locations in the file system outside of the project's location. These special folders and files are called linked resources.

Different tools that plug into the Workbench use their own specialized types of projects, folders, and files. 

Workbench
Navigator view
Resource hierarchies
Linked resources
Builds

Importing resources into the Workbench
Creating a project
Creating a folder
Creating a file
Creating linked resources
Closing projects
Viewing resource properties
Finding a resource quickly
Copying resources
Moving resources
Comparing resources