@hfpop: No idea, I've *never* used FTP to communicate with an eInk device, always scp/sftp.
I do build busybox w/ ftpd support, but I'm not quite sure I've ever actually tried it besides just making sure it accepted incoming connections

.
EDIT: Turns out I do have ftpd enabled on my end, and it still works, yay!
And I'm not seeing anything weird with hidden folders?
Code:
drwxr-xr-x 157 8192 Apr 21 23:11 .kobo-images
drwxr-xr-x 2 4096 Apr 30 2016 .adobe-digital-editions
drwxr-xr-x 8 4096 Jun 3 20:16 .kobo
lftp kobo:/mnt/onboard> ls -l .kobo
drwxr-xr-x 3 4096 Jun 3 20:16 upgrade
-rwxr-xr-x 1 308 Jun 3 20:16 manifest.md5sum
-rwxr-xr-x 1 81926607 Jun 3 20:16 KoboRoot.tgz
-rwxr-xr-x 1 32768 May 31 02:39 BookReader.sqlite-shm
-rwxr-xr-x 1 12608 Jun 3 20:14 BookReader.sqlite-wal
-rwxr-xr-x 1 55296 May 31 01:24 BookReader.sqlite
-rwxr-xr-x 1 32768 Jun 3 20:16 KoboReader.sqlite-shm
-rwxr-xr-x 1 61864 Jun 3 20:16 KoboReader.sqlite-wal
drwxr-xr-x 2 4096 May 1 2016 certificates
drwxr-xr-x 2 4096 Jul 22 2017 guide
-rwxr-xr-x 1 87 May 31 01:33 version
drwxr-xr-x 2 4096 Mar 22 2017 Kobo
-rwxr-xr-x 1 76 Apr 30 2016 device.salt.conf
drwxr-xr-x 2 4096 Apr 2 13:42 dict
drwxr-xr-x 2 8192 May 1 23:47 kepub
-rwxr-xr-x 1 66123776 May 31 01:32 KoboReader.sqlite
-rwxr-xr-x 1 25 Jun 3 20:14 affiliate.conf
lftp kobo:/mnt/onboard>
(Yes, in the time it took me to actually install an ftp client, I got synced the latest FW update

, so yeah, that was over WiFI).