Dude, I'm so damn happy to see this release! I'd been using 3DShell since Version 2.0.0 or so and this damn bug you spoke of where it'd just wipe the SD card completely had me so damn stymied last night and this morning! I lost every damn thing on my 3DS's SD card twice and had to copy back over one of my hourly backups!
You are such a damn lifesaver. Props to you!
EDIT: I will append this with a remark: Like others, I prefer having access to the .CIA option for the app, as I tend to only use the .3dsx version of 3DShell or any other homebrew as an emergency if I have to. Having it on my home menu makes me feel much more confident in accessing it on a regular basis to transfer files back and forth. As such, the .CIA option for installation and updating as well as the FTP option are vital to me, moreso than using insecure Samba sharing.