No! FTPEdit will never include spyware. Spyware is a misuse of the trust you place in software. The website and domain are paid for out of my pocket and since downloads are hosted on winsite, bandwidth remains nominal.

Turn off the backup option. Backing up renames the file and then uploads a new copy thereby resetting the permissions.

Version 3.0 of FTPEdit includes caching that keeps a local copy of the file so that opening recently used files is much quicker. You can disable this functionality in Settings|Options, or set it to expire the cache at the end of the session.

scp unfortunately does not support directory listings. The best way that I have found to secure communications from a Windows system is to use TeraTermPro with TTSSH and port forwarding. This will secure the communications channel, but all files will be transferred unsecure.