Manage files under version control
Add files to VCS
Open the Commit tool window Alt+0
Put any files in the Unversioned Files changelist under version control by pressing Ctrl+Alt+A or selecting Add to VCS from the context menu. You can either add the entire changelist, or select separate files.
If you have enabled VCS integration for your project, CLion suggests to add each newly created file under version control (you can change this behavior in the Settings/Preferences dialog Ctrl+Alt+S under Version Control | Confirmation). If you want certain files to always remain unversioned, you can configure your VCS to ignore them.
Check project files status
CLion allows you to check the status of your local working copy compared to the repository version of the project. It lets you see which files have been modified, which new files have been added to the VCS, and which files are not being tracked by Git.
Open the Commit tool window Alt+0
The Default changelist shows all files that have been modified since you last synchronized with the remote repository (highlighted in blue), and all new files that have been added to the VCS but have not been committed yet (highlighted in green).
The Unversioned Files changelist shows all files that have been added to your project, but that are not being tracked by Git.
Track changes to a file in the editor
You can also track changes to a file as you modify it in the editor. All changes are highlighted with change markers that appear in the gutter next to the modified lines, and show the type of changes introduced since you last synchronized with the repository. When you commit changes to the repository, change markers disappear.
The changes you introduce to the text are color-coded:
line added.
line changed.
line deleted.
You can manage changes using a toolbar that appears when you hover the mouse cursor over a change marker and then click it. The toolbar is displayed together with a frame showing the previous contents of the modified line:
You can roll back changes by clicking 
and explore the differences between the current and the repository version of the current line by clicking 
.
Instead of reverting the whole file, you can copy any part of the contents of this popup and paste it into the editor.
Delete files from the repository
If you delete a file that is under version control, it still exists in the repository until you've committed the changes. The deleted file is placed to the active changelist, and is highlighted with grey.
Select a file in the Project tool window, and press Delete, or choose Delete from the context menu.
In the dialog that opens, you can choose whether you want to delete this file without searching for usages, or to perform safe delete to make sure that you are deleting an unused file by checking the Safe delete option.
If any usages have been found, the Usages Detected dialog will popup listing them. You can view these usages and remove references to this file before deleting it.
Commit the changes to the repository.