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accurate branch
Being a pure, plain decompilation of the original Doukutsu.exe file (v1.0.0.6),
there should not be much to say about this branch's philosophies:
Goal
The end-goal is for the project to be able to produce an .exe file that is
identical to the original. This means that there should be no custom code,
decompiled code should ideally be made to produce the same assembly code as the
original, bugs should be left intact, etc.
Another goal of the project is to document Cave Story's inner-working, so code
should be reasonably-annotated. Likewise, bugs should be documented, and fixes
provided wrapped in #ifdef FIX_BUGS conditions.
Accuracy to the original source code
Personally, I do aim to make the decompiled code functionally-accurate to the original, down to generating the same assembly code, but I do not aim for visually-accurate code.
Despite this, I do try to preserve the original function/variable names, variable-declaration locations, and source file naming.
Part of the reason why I do not aim for visually-accurate source code is that we know from the Organya source code release what Pixel's code-style looked like, and I find it extremely hard to read.
Language
Cave Story's developer (Pixel) primarily speaks Japanese, but his code's variable/function names are mostly written in English (with a few rare instances of Romanised Japanese).
The Organya source code release indicates that Pixel wrote his comments in Japanese, however, in this project, I prefer them to be written in English.
The English employed in this project is a mix of American English, Canadian English, and British English.
portable branch
This branch takes a different direction to the accurate branch, but they still
share many core philosophies:
Goal
While accurately-reproducing Cave Story's original code is still a priority, the main focus of this branch is to port the game to other platforms, while also preserving the game the way it was experienced back in 2004.
Essentially, this branch exists to provide a purist Cave Story experience without requiring an old Windows XP computer.
Notably, this means that bugs should still be left intact. However, bugs and other coding errors that affect portability should be fixed.
For comparison, I believe this branch shares many parallels with the Chocolate Doom project. Follow the link below to see that project's list of philosophies, which may be applicable here:
https://github.com/chocolate-doom/chocolate-doom/blob/master/PHILOSOPHY.md
Custom code
Cave Story's original source code was written in C++, but stylised like C89 (with a number of exceptions). Custom code added to the project should follow suit, but the C-style doesn't have to be C89 - personally, I prefer to write in the subset of C99 that C++98 allows.
I prefer compiler-specific code to be avoided, since more-portable code benefits all compilers, and keeps the codebase free of clutter.