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I am new to things like FTP and such. I have a data collection program on my Pi. I need this data to be extracted by a PC with in my network, but I do not want them accessing all the other folders. My problem is that I'd like for a certain folder only to be accessible through a third party FTP app. When just using Windows Explorer, everything is Ok. When I check with Filezilla, I see all my hidden files and important files. I do have restrictions like cannot use Dropbox. This needs to be a direct file transfer.

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The solution is based on VSFTPD with anonymous login assuming the system is Raspbian but you can also set user specific login and limit the directory like this. Install vsftpd from software repo and run sudo nano /etc/vsftpd.conf and change the anonymous login option and add directory options as following,

# Allow anonymous FTP? (Disabled by default).
anonymous_enable=YES
no_anon_password=YES (if no, the password will be anonymous by default)
anon_root=path_to_your_desired_directory

and then run sudo systemctl restart vsftpd to take those settings into effect. With the above configuration you can set only your desired directory to be discoverable to ftp.

And you can see for further information here.

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