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To do this download the installer and run it with the [http://www.eecs.wsu.edu/paint.net/doc/2.6/Help/en/UnattendedInstallation.html options] you want making sure to add "/createMsi":
<pre>
Paint.NET.3.365.Install.exe /createMsi CHECKFORUPDATES=1 CHECKFORBETAS=0 JPGPNGBMPEDITOR=1 TGAEDITOR=1 ALLUSERS=1 DESKTOPSHORTCUT=1
</pre>
This will create a folder called "PaintDotNetMsi" with two files in it: "PaintDotNet.x64.msi" and "PaintDotNet.x86.msi". Copy the "PaintDotNet.x86.msi" to your server as "paint.net-3.36.msi".