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Unzip the attached archive and run xbuild in the demo/ directory. The key is that we have two files, namely a/foo.cs and a/b/bar.cs, and a .proj file with an item <Source Include="**/*.cs"/>.
a/foo.cs and a/b/bar.cs occur once each in @(Source).
a/foo.cs occurs 2 times and a/b/bar.cs occurs 3 times in @(Source).
Created attachment 3142 [details]
A set of files to reproduce the bug
Mac OS X 10.7.5, Mono 3.0.2, XBuild 3.0.2
$ uname -a
Darwin ******** 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
$ mono --version
Mono JIT compiler version 3.0.2 (master/9e7f206 Wed Dec 5 08:41:22 EST 2012)
Copyright (C) 2002-2012 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
GC: Included Boehm (with typed GC)