I often switch between MonoDevelop on Linux and VS2010 with the same code base so I'm forever having to click do not convert line ending. Is there an option to set a default answer in MonoDevelop to prevent this dialog from popping up?
Found it...
Edit > Preferences > Source Code > Code Formatting > Text File > Line Endings
For v2.8.2:
Project > Solution Options > Source Code > Code Formatting >Text File > Line Endings
And for 4 (a.k.a. Xamarian Studio):
Tools > Options... > Text Editor > General > Coding > "Line ending conversion:"
In MonoDevelop 5.9.6 I found this option under :
Project > Solution Options > Source Code > Code Formatting