Summary
To stage or unstage all of your files in GitHub Desktop, use the top checkbox in the left pane. To stage or unstage individual files, use the checkbox next to each file name. The files with a checkmark will be included in your next commit.
Details
In Git, staging is the process of determining which files you want to commit and which files you want to leave out of your commit. Staging a file means you’re adding it to a list of files that will be committed. It’s an intermediate step between writing your code and committing your files.
Staging is especially useful in cases where you’ve modified multiple files since your last commit but only want to commit some of them.
References
Selecting changes to include in a commit | GitHub Desktop Help