Whatever you do in CLion, you do that in the context of a project. A project is an organizational unit that represents a complete software solution. It serves as a basis for coding assistance, bulk refactoring, coding style consistency, and so on.
CLion supports the following project formats: CMake, Makefile, JSON compilation database, and Gradle. For more information, refer to Project formats.
A project in CLion is represented in the Directory Based Format. The project directory contains the .idea directory (not visible in the Project view of the Project tool window), with the following files:
.iml file that describes the project structure.
workspace.xml file that contains your workspace preferences.
A number of xml files. Each xml file is responsible for its own set of settings, that can be recognized by its name: projectCodeStyle.xml, encodings.xml, vcs.xml, and so on.
Thus, for example, adding a new run/debug configuration and changing encoding will affect two different xml files. This helps avoid merge conflicts when the project settings are stored in a version control system and modified by the different team members.
Project root directory
Any project in CLion should be encapsulated within the project directory, referred to as the project root. It contains all the project files and subdirectories, including configuration, data, source, and other files related to the project.
Project root directory contains one or more files of project description, which are also the inputs to the build system: CMakeLists.txt for CMake, compile_commands.json for compilation database, Makefile for Makefiles, and build.gradle for Gradle.
When you open a project, CLion treats the location of the top-level configuration file as project root. Also, in the case of CMake, when you create a new CMake project, CLion places the CMakeLists.txt file under the root.
If you need to change the project root directory, follow this instruction.