Add -mergebyhash command line option when running PartCover, to avoid trying to add the same assembly to the code coverage results more than once. See http://community.sharpdevelop.net/forums/p/22003/56296.aspx

src/AddIns/Analysis/CodeCoverage/Project/Src/OpenCoverApplication.cs

@@ -104,7 +104,7 @@ namespace ICSharpCode.CodeCoverage
 		string GetArguments()
 		{
 			// IMPORTANT: https://github.com/sawilde/opencover/wiki/Usage
-			arguments = new StringBuilder("-register:user ");
+			arguments = new StringBuilder("-register:user -mergebyhash ");
 			
 			AppendTarget();
 			AppendTargetWorkingDirectory();

src/AddIns/Analysis/CodeCoverage/Test/Testing/OpenCoverApplicationTests.cs

@@ -163,7 +163,7 @@ namespace ICSharpCode.CodeCoverage.Tests.Testing
 			ProcessStartInfo processStartInfo = openCoverApp.GetProcessStartInfo();
 			
 			string expectedCommandLine =
-				"-register:user -target:\"d:\\sharpdevelop\\bin\\Tools\\NUnit\\nunit-console-x86.exe\" " +
+				"-register:user -mergebyhash -target:\"d:\\sharpdevelop\\bin\\Tools\\NUnit\\nunit-console-x86.exe\" " +
 				"-targetdir:\"c:\\projects\\MyTests\\bin\\Debug\" " +
 				"-targetargs:\"\\\"c:\\projects\\MyTests\\bin\\Debug\\MyTests.dll\\\" /noxml\" " + 
 				"-output:\"c:\\projects\\MyTests\\OpenCover\\coverage.xml\" " +
@@ -187,7 +187,7 @@ namespace ICSharpCode.CodeCoverage.Tests.Testing
 			ProcessStartInfo processStartInfo = openCoverApp.GetProcessStartInfo();
 			
 			string expectedCommandLine =
-				"-register:user -target:\"d:\\sharpdevelop\\bin\\Tools\\NUnit\\nunit-console-x86.exe\" " +
+				"-register:user -mergebyhash -target:\"d:\\sharpdevelop\\bin\\Tools\\NUnit\\nunit-console-x86.exe\" " +
 				"-targetdir:\"c:\\projects\\MyTests\\bin\\Debug\" " +
 				"-targetargs:\"\\\"c:\\projects\\MyTests\\bin\\Debug\\MyTests.dll\\\" /noxml\" " + 
 				"-output:\"c:\\projects\\MyTests\\OpenCover\\coverage.xml\" " +