The mono debugger, MDB, does not yet work on Mac OS, so MD cannot use it to debug Mono applications. Please note that if there are no debugger adapters in the MD, there is no "Debug" command, only "Run".
AFAIK, MacOS MDB support should be in Mono 2.6, although I expect it to be somewhat experimental. When this is shipped, we can enable the addition of the MDB adapter in MonoDevelop.
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