I got this weird error after booting up Raft through Steam. It says File Corrputed! This application has been manipulated and maybe its infected by a Virus or cracked. This application won’t work anymore.
I saw a similar post and the Moderator said that they don’t condone pirated games and closed the thread. That’s not a great way to figure out what is going on. WeMod worked just fine yesterday with a BOUGHT COPY of Raft from Steam. Its your Application and not the game.
Welcome to the community. 
Sorry to hear you’re having an issue. However, we have not recently received any similar reports of this from our millions of active users, this is the only one recently.
This error message is not from WeMod.
Your error message gives you three reasons why the game might not be working (corruption, virus or cracked). So I’m not sure why you’re focusing on one of those three reasons, maybe it is or possibly was cracked in the past after all? 
We get it, maintaining a gaming habit is expensive these days, so some people decide to go down the unlawful route, but still, we can’t support it ourselves, we are a law-abiding business.
If your game is cracked (including if you’re using a save file from a cracked game on a purchased copy), then there’s nothing WeMod can do for you. This thread explains why (click).
As the error states, it’s also possible that your game is corrupted. Corruption happens on Windows machines for absolutely no reason, completely randomly, and at no fault to yourself or anyone else other than Microsoft. The solution here would be to either restore the integrity of the game files (Google will provide instructions in seconds), or delete and reinstall the game.
This error is also potentially caused by your antivirus suddenly deciding to block something. Add both the game and WeMod files as an exception in your antivirus program (just in case - before you say “I don’t have an antivirus” - you do. Windows Defender is an antivirus and it is on every PC and cannot be removed as it is embedded permanently into the operating system).
And do a deep virus scan of your PC. I’d also recommend getting MalwareBytes to run alongside your antivirus, as antiviruses tend to not be as good at detecting malware as they are with viruses.
You might also be banned for trying to cheat in multiplayer modes. Having not played Raft before, I’m not sure if there is multiplayer or not. In this case, you’ll need to contact the game developers and politely apologise/grovel.
I uninstalled and re-installed WeMod and it works fine now. It was super weird. There is a multiplayer, but its server based so you can just not have it be multiplayer. I double checked my anti-virus and it was fine and my Firewall was allowing the game and WeMod to work. The error popped up on several different games that are expressly single player as well. But thanks for the reply. I did get it to work again. I don’t pirate games. Its shifty at best and downright dumb at worst. I always pay for my games.