http://getmdesktop.com
Looking through the Github project i learned that it was build upon scripts from AutoHotKey that where compiled to exe.
http://www.autohotkey.com
Wanting to find out more about the script language i fell upon this little joy that enables transparency on an active onenote window. Im now using it for OneNote transparency on my smaller laptop.
http://www.autohotkey.com/board/topic/15949-script-to-make-onenote-transparent/
#IfWinActive, ahk_class Framework::CFrame LSHIFT & F1:: WinGet, _T, Transparent, A _T := _T = 150 ? 255 : 150 WinSet, Transparent, %_T%, A Return
Install autohotkey and after starting it the first time you get a script window that autoruns with autohotkey at startup, just past the above script into this file reload the script and you have transparency on the active OneNote window using left shift and f1.
If you want to try some more transparency you could look into
http://poojanblog.com/blog/2008/08/autohotkey-transparency-script/
Autohotkey rocks.
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