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I have recently been using MonoDevelop 2.6 alongside Visual Studio 2010 and noticed a somewhat annoying issue. Inside the solution file, VS2010 commonly adds the following line:
<Import Project="$(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v10.0\WebApplications\Microsoft.WebApplication.targets" />
For one reason or another, when MonoDevelop opens the same solution it adds the following line in addition to the previous line:
<Import Project="$(MSBuildExtensionsPath)\Microsoft\VisualStudio\v9.0\WebApplications\Microsoft.WebApplication.targets" />
Afterwards, VS2010 cannot open the solution because the latter path does not exist on the machine with only VS2010 installed thereby breaking the solution file for VS2010 and requiring manual modification each time it is opened.
Fixed in git master (will be 2.8.7)