This is all pretty simple and quick. Make changes, repack each time you're finished, and then next time you launch the game the changes will show up. If your changes didn't show up, make sure that you're packing up the right files from the directory you think you're working with.

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Using Paxtez's Mod Manager

Select "Rebuild ARC File". When that's done, select "Copy to Steam". That's it - you're ready to play!

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Using CollectionTool

Double-click CollectionTool.bat. Select "Marvel vs Capcom Collection", select "Marvel vs Capcom 2", select "Game", then select Repack. That's it, you're ready to play!

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Using ARCTool

Run: arctool -c -pc -txt -v 7 YourArcNameFolder Then copy the ARC file that it generates to your "nativeDX11x64\arc\pc" game folder. That's it, you're ready to play!

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Troubleshooting

If you have any problems, you can always restore your ARCs from the backup copy you made earlier. Don't forget to save copies of your changes that you really like to: having checkpoint backups saves a lot of time and frustration.

If you forgot to make a backup copy, you can repair your build using Steam. Go to Library : Home. Go to the Marvel vs Capcom Fighting Collection entry. On the same line where it says "Play", there is a gear near the right side. Click Manage : Properties... . Go to "Installed Files". Click "Verify integrity of game files": that will have Steam restore the original files.