No problem. I like the Decrypt9 directory instead of everything on root. It makes my filesystem cleaner. I was able to get the xropads working once I found out the correct folder.
I'm thinking about making the work directory an option. I do prefer having all out of the way and so do you, but it's almost sure that this will lead to confusion. Plus, every other software out there wants the "slot..." file, "ncchinfo.bin" file and others in the root directory.
@Shadowtrance:
I still think that how the restore NAND option is accessed in the menu is too dangerous. If there is a chance something bad happens, it will happen, and just having to press an additional button is not a good layer of security. Picture an user accidentially triggering that option, who panics and force shutdowns their 3DS. Even Roxas75 gets criticism from time to time for including the NAND restore and inject options in a submenu. Also, the NAND restore option (in my opinion) should not be used by someone who doesn't have a hardmod at all. As of now, the restore NAND option is the only really dangerous option in Decrypt9, for all others basically nothing bad can happen, even with bad input files, force shutdowns and otehr stuff users might come up with.
I'd suggest you make it 'more impossible' to trigger that option by accident. For example, by starting Decrypt9 in a 'safe mode', which the user has to actively switch to even get the NAND restore option in the menu. Or, put a disclaimer, with visual clues about danger (f.e. exclamation mark, red letters...) between the menu and the execution of the NAND restore option. Then require the user to input a key combination to continue. Or do two versions of Decrypt9, one with, one without the option.
I put some work into the ncchinfo_gen.py scripts. And, yup, ncchinfo v4 is not backwards compatible because the entries are 8 bit longer and include the titleId. It would be pretty easy to write a ncchinfo v3 -> v4 converter though. But, does that make sense? Do people really have old ncchinfo.bin files lying around that they still use to generate XORpads? Also, keep in mind that the CTRdecryptor option (once I finish that) will lead to people using the ncchinfo.bin format less anyways.
The seeddb mystery... I posted
here hoping to get some people onboard for solving that (I don't think Archshift will reply on Github). I really think it should be possible to generate the seeddb.bin from nand:\data\<id>\sysdata\0001000f\00000000, but you'd have to be on a recent FW version (which I can't do) to even get that. Also, I'd like to know if that file is identical for every 3DS or if it is unique. Not a pressing issue, but knowing that you've got three 3DSs with hardmods lying around, you are one of the few persons who can find out on their own

.
Last point - decryption (and encryption, of course) of TWL - I'm at it. Can't say much about yet, cause I'm still trying to figure out how to handle the different endianness of the TWL partitions. Check out the last few posts
here if interested.