When you load a project its contents and settings are accessible in three main sections in the Project Explorer on the left: Table of Contents, Project Files and Configuration.
The Table of Contents or "TOC" is a hierarchical tree of entries that define the structure of your project, organizing your topics into chapters and sub-chapters. Most TOC entries have direct links to topic files in the Project Files section. (You can also create additional TOCs with different structures for the same project.)
The Project Files section provides access to the actual files that make up your project.
The Configuration section stores all the settings associated with your project.
Topic entries in the TOC are actually links pointing to matching topic files in the Topic Files section. The actual topics are only stored in the Topic Files section.