By default, Pathagoras will filter out all 'non-document' files in the designated folder. If you wish to always display every item in the selected book, check the appropriate box found under the 'All Files?' tab.
If sometimes you want to display all files but sometimes you don't, leave the 'All Files?' check-box unchecked. When you are in a document assembly session, selected the desired book that you want to display and click Next. The 'normally' filtered display will be presented in the Clause Selection Screen. Now, click the Show All button toward the lower left side of the screen. The left ("Available Files") panel will be repainted to show all files in the folder.