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EFT stores its ftp.cfg in a hidden folder named %systemroot%\ProgramData. (To show it in Windows Explorer, click Tools > Folder Options > View tab, click Show hidden files and folders, and then click Apply.)
C:\Program Files\Globalscape\EFT Server
or
C:\Program Files\Globalscape\EFT Server Enterprise
Application data is stored in
C:\Documents and Settings\All Users\Application Data\Globalscape\EFT
or
C:\Documents and Settings\All Users\Application Data\Globalscape\EFT Enterprise
Resource files used to create the Web pages are stored in \contrib\EFTClient
Everything necessary for the Web site that is not contained in the resource folder is stored in \public\EFTClient
Files used by Web Services are stored in \public\EFTClient\WebServices.
When upgrading, previous files are backed up to web/backup/EFTClient
Custom files are stored in \custom\EFTClient (empty by default). The EFTClient folder in this directory contains customizations that apply to all Sites on a server. To customize files for the Site, create a directory structure in the form [SiteName]/EFTClient/ in this folder. The Site folder should hold just those files that contain customizations for that Site. The best practice is to have only customized files in this folder and to leave the original files as they were when installed in the \web\public\EFTClient folder. WTC and PTC files can be modified independently.
(For assistance editing the WTC interface, refer to Rebranding (Customizing) the Web Transfer Client.)