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In order to run MonoDevelop in Monoppix you need to do the following. Goto Start Applications, Quick Broweser, Root Directory, KNOPPIX, usr, bin and choose /KNOPPIX/usr/bin and select "Open In Terminal". In the console window write "monodevelop" without quotes to start the IDE.

I really like the IDE, still exploring it, but according to me its my Mono VS :). However I am still unable to compile and run applications, but will give it another try sometime later.