Well, thank you for looking at my code and giving your opinion, I appreciate it  Let me answer you.

Still using the deprecated flat binary format with objcopy

Hum... sorry about that, but I don't know what you are talking about I'd be glad you enlight me

Using nl_exec incorrectly: argv[0] is the program itself, argv[1] the first parameter

Actually I read on hackspire :
"args[] must not include the program name (argv[0]) nor the terminating NULL argument"
Since .py execution is working, I guess im doing it the right way.

Placing the config file outside of /documents the user can't delete it in a usual way. IMO that's very annoying, each file slows the calc down.

I don't think this a real issue, since the config file's aim is to be not deleted ; and even if you do so, it will be re-created next time you launch the program. Therefore, I admit it's indeed more convenient for the user to control the file.

Not checking the return values of fread

You just spotted my laziness 
But since the config file is hidden and can't be edited by usual ways, it should always has the structure I gave him, no ?

Saving the file as temporary file when running as python script

Why is this a problem ?  It enables the user, when he has modified a .py file, to test his changes without having to save his current work. There's no way to do it otherwise.

In NoteWriter.c line 405 there's an 'n' missing.

Thanks for this

On line 633 there's an invalid character literal: '\25' isn't 0x25 but rather "25", which is not a single character, I guess you meant '\x25'

I have to thank you for this too. Actually Notewriter 1.0 was using this '\25' character for indicating line feeds, which wasn't very proper. The 2.0 version was not intended to use this character anymore, and even if it still supports his use, this '\25' was unintended.

Your WinBox framework looks useful, but there's no documentation for it and IMO it would be 100x easier to use if it was coded in C++.

Actually I made a documentation, but sadly its in french I wanted to provide an english version too, but since I was not on omnimaga at this time, I told myself it would be some harassing work for almost nothing.
If you want to take a look nonetheless, it's available here, with Winbox 1.2 : http://tiplanet.org/forum/archives_voir.php?id=10587
I would have prefer to code Winbox in C++ too, but when I started the project, years ago, C++ was not fully implemented for the nspire (or I've been misinformed).

You're using quite a few triple-pointers: "Widget ***wFiles", I haven't seen those in the last 20 years and I'm only 17.

The last, but not least ! I dont know if I should be ashamed, or proud... My father, who is an engeneer and develop projects for more than 20 years, also told me triple pointers were never necessary. I guess I just found a specific case where they are necessary.

That would be cool as it is a pure python library, but im having troubles actually making it useable on the ti nspire CX CAS... i cant transfer the library over due to restrictions on the software, as it obviously has to be a TI Nspire file, and obviously the files i need to import are .py... any ideas how this may be available to do?

I'm not a python-user, so I'm not awared about how to import a python library.
Do you only need to transfer the .py files to the calc to use the library ? If that is so, I'm already working on a solution.