Ok so I fixed the issue. Not sure of the cause, but I was able to just delete all the unneeded folders. Just a quick question, what scripts in the init.d folder are for a2sd other than the obvious script?
Addition: Isn't there away to move data to the sd-ext as well?
I wrote up this really awesome reply before i realized your response. since i dont believe in waste, i'll go ahead and post this lol. (who knows, maybe it will help someone somehow)
So I went further into to rabbit hole to do some more investigating and it seems to just keep going. I stopped counting at 12 folders in. Would some one mind look into the /system/sd/app, or any of those folder and let me know?
I think you may be following a rabbit trail here. Android, I don't know much about. Linux on the other hand, I've had many years of experience with (though I'm still an idiot so dont take this as me self proclaiming to be an expert).
I've seen many instances like this where either a symlink or a hard link are at fault, linking back to its own folder. It will do all sorts of weird things (like make things think you're out of disk space, never be able to calculate how massive that never ending folder is, etc).
Since linux is lacking certain limitations that windows has (folder nesting character size limits), it's likely that it will be "truly" indefinite.
The good news is, any time I've ever run across this I have been able to rectify it easily. Just get a shell (adb or on phone will work fine), then get to the directory in question. Do a ls -al and see if it is indeed a symlink. Even if it isn't, you should still be able to do a recursive delete-anything style delete on the directory. Here's a little bit more specific directions:
make a full backup (no, really... don't trust my abilities lol)
open a shell
[enter root]
su -
[change to directory]
cd /system/sd/app/
[discover if this is truly a hard link or symlink]
ls -al
[if you see something to the effect of this, you've confirmed it's just a link]
/system/sd/app/ -> /system/sd/app/
[if not, that's ok, here's the magic delete you no matter what you say command]
del -alR app/
[honestly, i don't recall if the trailing / is required, i'm so used to tab completion i don't even think about those things]
if it is truly a deeply nested/repeated folder, that command might take some time to complete, but it can't take forever because the card only has so much space. once finished, reboot and see if it comes back.
if it comes back, then you *know* there is an app/script/init.d/something putting it there. from that point the easiest solution might just be to begin from scratch and be sure you don't put anything conflicting.
if you have had conflicting software (as in, trying to perform the same function) the uninstaller scripts may not have worked properly which may require manual cleaning up of files. manual cleaning up is really not too bad if you know what to expect in there but i wouldn't have the first clue on what to expect on an android device.