Apart from storing files, Zoho Projects also allows you to move, delete, sort and upload latest versions of a file.
In Documents tab, mouseover on a particular file displays file action menu
This uploads the latest version of the file with a new version number i,e if the previous version is 1.1 means the latest one is stored with a version number 1.2.
You need to store files related to a particular module all in one folder. For Eg: All marketing related files needs to be stored under Marketing folder. For this move file option comes handy.
That's it. The file is moved to the destination folder
This deletes the selected file forever from the project workspace

Mouseover on the filenames column to sort the files in ascending / descending order.