Geneious documents are stored in a hierarchal arrangement of folders under the Local folder in the Sources Panel. Clicking on a folder will display its contents in the Document Table. Next to each folder name in the hierarchy is the number of documents it contains in brackets. When the Local folder or a sub-folder is collapsed (minimized), the brackets next to the folder shows how many files are contained in that folder as well as all of its sub-folders. In addition, if some of the documents in a folder are unread, the number of unread documents will also appear in the brackets.
To create a new folder, select the Local folder or a sub-folder icon in the Sources panel and either right-click (Ctrl+click on Mac OS X) and select New folder from the popup menu, or go to File → New → Folder. This will open a dialog where you can name your new folder. This folder will then be created within the folder you originally selected.
You can also delete, rename, move, export or change the color of a folder by right-clicking on the folder (or control-click on MacOSX) and selecting the option you require from the menu. These options are also available under the File menu. In Mac OS X, you can also use the plus (+) and minus (-) buttons located at the bottom of the service panel to create and delete folders.