CSE2 is a decompiled version of the original freeware version of Cave Story (Version 1.0.0.6). This allows for a greater ability to modify the game in addition to building newer executable files for other platforms.
There are two main branches actively being worked on. The "accurate" branch, which aims to be as close to the original executable as possible, and the "portable" branch, which is modified to have greater compatibility with other systems while still maintaining authenticity. For any system that isn't running Windows, the portable branch is the one to choose. A complete guide for compiling an executable on Windows can be found under "How to compile" at the forum thread linked below.
-- For more information, see the links below --
Latest release of portable branch (Downloads for Windows and Wii U)
GitHub Page (accurate branch)
GitHub Page (portable branch)
Thread on the Cave Story Tribute Site Forums
Discord Server
Cave Story: Tweaked is a fork of the abandoned "enhanced" branch of CSE2 maintained by ikuyo that focuses on adding additional options that improve playability. These mainly focus on adding accessibility options to the technical improvements introduced by enhanced. A complete list of features can be found on the GitHub page.
-- For more information, see the links below --
Latest release of Tweaked (Downloads for Windows in English and Japanese)
GitHub Page
Thread on Cave Story Tribute Site Forums
Page Last Updated: 2020.11.23