Use jdupes to replace duplicate files with hardlinks; this way instead of having 'Zero Hour\generals.exe' and 'Zero Hour Shockwave\generals.exe' and 'Zero Hour Contra\generals.exe' pointing to different parts of the hard drive and taking up a total of 18.5mb, all three will point at the same spot and take up the same 6.5mb of space. This will save you the space the base install takes up for all but one base install. Instead of taking up ~5.24gb, ZH, Contra, and Shw will take up ~2.88gb (folder properties will not reflect this as windows explorer doesn't recognize hardlinks, but disk properties will--right click the drive in 'this pc' or 'my computer' and go to properties to view total disk usage before and after linking files)
The command you want for jdupes is `c:\path\to\jdupes.exe -Lr "c:\path\to\Zero Hour" "c:\path\to\shockwave" "c:\path\to\contra" "c:\paths\to\other\mods"`.
For example, all my mods are installed in 'J:\games\c&c\mods\ZH' and ZH is installed via both origin and TFD, so I use `c:\programs\jdupes.exe -Lr "J:\Games\C&C\Mods\ZH" "J:\Program Files (x86)\Origin Games\Command and Conquer Generals Zero Hour\Command and Conquer Generals\" "J:\Program Files (x86)\EA Games\Command & Conquer The First Decade\Command & Conquer(tm) Generals\generals.exe"`
You can get to the command prompt by running cmd.exe from the start menu (or run menu).
You can append as many paths as you want to this command; just make sure to include the double-quotes around them if you have spaces or other special characters in them.
Tip: you can actually drag entire files and folders into the command prompt from windows explorer. This will add the full path to that file (including the name of the file itself and any necessary quotes) to the end of the current command line. So you can drag jdupes into the command prompt, type -Lr, and then drag each folder in--just make sure to add spaces in between paths.
You can usually get jdupes here: Github.com but at time of writing, you'll need this link, as the latest version has no downloads: Github.com
tomstefanou you may want to build this functionality into your application. It should be extremely simple to download and run jdupes.exe on the path the application uses.
Efreak
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