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$ export PATH=/opt/mono-3/bin:$PATH
$ export PKG_CONFIG_PATH=/opt/mono-3/lib/pkg-config
$ ./configure --prefix=usr
checking for mono... /opt/mono-3/bin/mono
checking for gmcs... /opt/mono-3/bin/gmcs
checking for pkg-config... /usr/bin/pkg-config
configure: error: You need mono 3.0.4 or newer
$ mono --version
Mono JIT compiler version 3.2.0 (tarball Tue Jul 30 21:08:00 UTC 2013)
Copyright (C) 2002-2012 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
LLVM: supported, not enabled.
This looks like a configuration issue. MonoDevelop doesn't depend on Mono being installed in a specific location.