Do not hide debug command bar if we are exiting the MonoDevelop

Fix issue with MonoDevelop not closing down properly if the debugger is still attached on shutdown.

Also removing MDMenuItem.cs that was not reverted properly in this commit: https://github.com/Unity-Technologies/monodevelop/commit/6ac03ff58accf22862ba28173c5430d1eee37e28

Which reverted this commit: https://github.com/Unity-Technologies/monodevelop/commit/55fea305d4303d921fd6812f22b4d4b408320e92

Notice there are only 10 files reverted, but 11 in the original commit.