Extract the files in the "assets.zip" archive in the game directory to a temporary folder. In that temporary folder, use a text editor to edit the "Hack.lua" file in the "AssetsScriptsGlobalFunctions" directory. Find the following line:
"local keys = _G.GATES[location].keys"
and change it to:
"local keys = 0"
Re-create the "assets.zip" archive using the modified file. This will change the number of keys of all gates in the game to 0. You will auto-hack all gates opened because you start with the gate fully completed.