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Sorry about that, I'm not quite used to Visual Studio and all the code shows up properly indented there for some reason.
The source code might have some screwed up indenting. Mod listings will be remembered after closing and relaunching, but settings such as the "Use Launcher" and "Exit after Launch" checkboxes will not be remembered after closing the manager. Try running as administrator to fix any issues encountered from this. The manager may not function properly if not given write permissions in the game directory. UNS4 doesn't have a launcher, so the checkbox doesn't exist there. The "Use Launcher" button does not work with a Steam copy of the game, as Steam will force the game to use the launcher regardless.
Check the boxes for any mods you wish to enable. Navigate to mods/(mod name) and insert the mod's data_win32 folder along with any other folders it uses. Fill in the name, author, and description for the mod. Start the manager and configure your mods (details below). Extract the contents of the archive to Steam Installation Folder)\steamapps\common\NARUTO SHIPPUDEN ULTIMATE NINJA STORM REVOLUTION\ for Revolution, (Steam Installation Folder)\steamapps\common\NARUTO SHIPPUDEN Ultimate Ninja STORM 3 Full Burst\ for UNS3FB, or (Steam Installation Folder)\steamapps\common\NARUTO SHIPPUDEN Ultimate Ninja STORM 4\ for UNS4. Download the zip from the releases page. You can install the manager either by downloading and compiling the source code from this repository, or downloading the latest release package for the corresponding game from here. The manager functions by copying the contents of enabled mod folders to the root of the game before launching, allowing the user to avoid lots of manual work in managing their mods. This is a simple mod management utility for the Naruto Shippuden: Ultimate Ninja Storm games, 3, Revolution, and 4 specifically, based off of MainMemory's SA2 Mod Manager.