Program Update Behavior

After the autoupdater runs and installs the updates it installs them into a new program directory. If version 1.0 was the base the next update creates a 1.1 sub-directory with the new .exe. Anyway to direct the update into the original install directory and overwrite the old data? A restart simply restarts the old program if I don't point it at the new directory. No big deal for me but my user shave trouble editing start directories on shortcuts and all other simple tasks.

Thanks

Scott