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I would suspect that most of the casual linux users out there install and use Wine because they are dual-booting with a Windows install and are not wanting to go through the POSSIBLE hurdle of installing programs through Wine. Those users will only have to deal with their install directory and nothing more.

I'm gonna post about how to use the command ln to create symbolically-linked (aka. sym-linked) directories from your user's emulated "C:\Program Files\" to the location of the actual install somewhere on your system. What does this do? Well, it allows Wine to always know where something is installed, for one (This greatly helps when updating games via Wine since the idea of "Program Files" will still apply). Two, it can help you save disk space should your hard drive be formatted into multiple partitions and the installed software is on a partition separate from your operating system.

IF( $your_interest == 'peaked' ) {

1. Enter your user's "C:\Program Files\" directory -
   $cd ~/.wine/drive_c/Program\ Files/
2. Create the directory -
   $ln -sf /path/to/installed/software/ Name\ of\ Software

}

... That didn't seem to take too long, perhaps I'll elaborate the teaching with an example.
NOTE: In the following, when "C:\Program Files\" or any other quoted paths appear I am making reference to the Windows-esque environment of Wine. So "C:\Program Files\" = /home/USER/.wine/drive_c/Program\ Files/.

STORY: I find installing Dawn of War presented me with a perfect example for the necessity of this article. During the install process the user doesn't get the option to change the install directory, so it installs to "C:\Program Files\THQ\Dawn of War\". For me, this means it's on my "Operating System only" partition, which is a partition of 10gigs and is better if ONLY used for the OS. So I want to move the "C:\Program Files\THQ\" folder to /mnt/games/ and then make a sym-link folder from "C:\Program Files\THQ\" to /mnt/games/THQ/ called 'THQ'. Of course, don't use my steps exactly because I made up the locations, except for the DoW install location, that's guaranteed. Anyways, on with the tutorial.

IF( $your_mind == 'confused' || $your_feelings == 'annoyed' ) {

1. Enter "C:\Program Files\" -
   $cd ~/.wine/Program\ Files/
2. Move the directory -
   $mv THQ\ /mnt/games/
3. Create link -
   $ln -sf /mnt/games/THQ/ THQ

NOTE: If you want to make sure this worked type: $ls -l. You'll know it worked because you'll see "[...] THQ -> /mnt/games/THQ" and it'll most likely be the color blue.
}