Comments - Matiiou

Problem with the hyperlink "our website".
Anyway, looks great, downloading now and reserving my Wednesday's work break to taste this new release.

To keep the original files from being overwritten, just follow the files structure described.
The batch will only be a launcher for the mod. That's all.

I just explained you how to do : you have to create a mod folder such as :
. <Path>\Crysis\Mods\SuperPowers\Game
. Your SuperPowers Folder must contain a info.xml written like this
--------------------------------------
<?xml version="1.0" encoding="utf-8"?>
<Mod Name="SuperPowers" Version="1.0" Screenshot="Mod.jpg" Description="SuperPowers" URL="https://www.moddb.com/mods/super-powers-mod-2-complete"></Mod>
--------------------------------------
. You can add a file Mod.jpg to have a splash screen on launch
. You can create a batch file of a shortcut to make it easier for players to launch you mod. This file, could be name SuperPowers.bat and must contain :
--------------------------------------
@echo off
..\..\bin32\Crysis.exe -MOD SuperPowers
--------------------------------------

To resume, you'll have the following structure
<Path>
..|_Crysis
....|_Mods
......|_SuperPowers
........|_Game (the actual game folder you published)
........|_info.xml
........|_Mod.jpg
........|_SuperPowers.bat

Why haven't you packaged it as a mod ? Unpacking it from the archive means to overwrite default files of Crysis.
It could be easier and cleaner if you just create a SuperPowers directory containing your Game folder and a simple info.xml (and why not a .bat to launch your mod).