Hello, again. I have yet another issue with my calculator.
Recently, I installed the Nover 3 auto-overclock. Around that time, my calculator would not open any files that were specified to be opened with a program in ndless.cfg.tns. I don't think this is Nover's fault, as when I renamed the "startup" folder in the "ndless" folder and rebooted, the problem still occurred. For example, when I try to open a .txt.tns file, it states that the file type is not supported, while nTxt can open it manually just fine. More importantly, I can not open any .ll2.tns files, which means I can no longer run Linux (much more important than any typing program ). Any help with this issue would be greatly appreciated.

Also, I'm not sure if this should be asked here, or in Ndless' Github issues section, or somewhere else entirely? Hm...

Can you attach your ndless.cfg.tns file?

Sure, it's attached to this reply.

The only thing I can think of is that your use of Nover corrupted the filesystem. You can try backing up your calculator and reformatting from the maintenance menu. Also, I would suggest posting on the Github issues, where you will get faster answers.

Okay, thank you. I will attempt such a feat when I have the time.

EDIT: Okay, so, I formatted the entire system, but when I try reinstalling nLaunchy, the TI software says that the 3.1.0 OS is corrupt. I've redownloaded it several times, to no avail. Is this my calculator's fault, or my computer's? Thank you.

EDIT2: It seems the farthest down on the OS line I can go is 3.6.0 (I can't downgrade to 3.2.4 or lower). The "About" button in the "Status..." section reports my boot2 as 4.0.3, however, nsNandMgr reports both my boot1.5 and boot2 as 4.3.49! I have never updated to 4.3, and I am still able to use nsNandMgr to set the minOS to 0.0.0.0. Any help would be much appreciated.

I'm assuming you have hardware revision I or earlier. In that case, you can use nsNandMgr to flash boot2 3.1. Do not attempt this if you have hardware revision J or later!

Okay, I flashed a boot2.img from TI-Planet using nsNandMgr, and by some miraculous force my calculator didn't brick... Except, after I rebooted my calculator, both the "About" button and nsNandMgr report my boot2 to be 3.2.4!? I'm so confused...
Also, I have a revision A calculator, and I would really like to not brick it (past the redemption of the fabled RS232), not only because it supports nLaunchy, but because it's easier to hold (heavier) and the screen isn't as blue as the newer ones.

Because the OS flashes a version of boot2 (unless you ran TNOC on it before installing). Just flash boot2 3.1 again and install nLaunchy. Don't reboot your current OS.
https://github.com/Excale/nLaunchy#-cx-installation-see-above-for-clickpad-and-touchpad-

Oh, okay. I sure hope my configuration issues are fixed! I'll report back with the results after I'm finished transferring everything back to the calculator.

EDIT: No!! It didn't work! I tried opening a nFrotz file (.z.tns), and it said it wasn't supported! I didn't install Nover yet, thinking that might've been part of the problem, but I guess it wasn't. The only files that open are gbc4nspire files, but that's it - not .txt.tns, not .ll2.tns, not .py.tns (well, I haven't tested this one, but I can assume so). It's quite a problem! I suppose I could try loading the same file system onto my revision V calculator, and share how that goes.

EDIT2: It didn't work? I'm not sure what's wrong now... Maybe it's the way I've organized my files? I have nested folders, some going to five directories deep, but I'm not sure how that would effect the loading of programs... At least I know my calculator isn't broken. The newer revisions just feel so uncomfortable...

Here's my file system, in case you want to test it.

Is ndless.cfg.tns in the right location? It should be in /documents/ndless/ndless.cfg.tns

Yes, it's definitely in the right location, sitting with ndless_resources.tns and nover.cfg.tns, and various other files.
I edited my above post to include my file structure, in case you wanted to test it.

EDIT: Wait, could my ndless-transfer folder be the issue? Seeing as it also has an ndless.cfg.tns. I was using the folder to transfer ndless to other Nspires someone wants "hacked", but I've never actually seen anyone else with one (except some person I don't know), so it wouldn't be too bad if I had to delete it.

EDIT2: Haha, wow, after all that, it was the ndless-transfer folder! 
I deleted it, and everything works now. I'm very gracious that you stayed with me through this adventure!

Taking a look at the Ndless source code, it does indeed search all of the /documents directory for a ndless.cfg.tns file. Perhaps this behavior should be changed?

Well, I don't think it's really required to change it, seeing as I don't know many people who wouldn't put ndless.cfg.tns in the /documents/ndless directory. Besides, the ndless config could just be transferred directly from the ndless directory, instead of some other directory.