When you choose "File > Make Packager Zip..." in Pageflex Studio, every file that is in the same directory (folder) as the Project File (.pf) will be added to the Zip file. Since the native files, any zip files, or other supporting documents will not be needed on the server, it is a good idea to store them in a separate folder so that they will not be included with the upload. In fact, you should really only have the files that are specifically needed by Pageflex in one folder, and keep all other files in a separate folder. Some examples of files that are used by Pageflex have the extensions .pf, .xdt, .tsl, .xft, and .xat. Obviously, you also want to include any images that are used in your project. Some examples of files you should move to a separate folder are files with the extensions .indd, .qxp, and .zip. Additionally, there is no need to save your fonts in that folder because the packager will automatically find them on your computer and include them in the zip file for you.