The FRC robot software repo uses a folder structure that makes it easier to find the code you want to modify as well as similar code that can be used as examples. Most of your work will be done in the source (src) folder, but at times you will need to look at files in other places. The src folder is broken down into a lower-level folders to organize the code. In Java this folder structure matches the package hierarchy.
There are many files and folders that are necessary for the software to build and run, but generally these are setup for you by WPILib or the robot template. Below is an example from the template along with a list of folders you where may need to work (listed from top to bottom). At times there are other miscellaneous files stored in root directory for things like settings for the dashboards or preferences.