I had the same issue but didn't want to modify things outside of the source tree in order to get this to work. Adding files to C:\Program Files... means that you have to do this manually on every dev machine to get the same behavior.
I did three things:
1) Created a Custom targets file which I import into every C# and/or VB/F# project in my solution by adding the following to each proj file:
<!-- Rest of project file -->
<PropertyGroup Condition="'$(SolutionDir)' == '' or '$(SolutionDir)' == '*undefined*'">
<!-- Relative path to containing solution folder -->
<SolutionDir>..\</SolutionDir>
</PropertyGroup>
<Import Project="$(SolutionDir)CommonSettings.targets" />
2) Added a clean target which gets called after the real Clean (using the AfterTargets attribute from MSBuild 4.0):
<Target Name="CleanCs" AfterTargets="Clean">
<Message Text="Deep cleaning C# project..." />
<CreateItem Include="$(OutDir)**\*.*; $(ProjectDir)\obj\**\*.*; $(IntermediateOutputPath)**\*.*"
Exclude="**\bin\**\*.vshost.exe; $(IntermediateOutputPath)**\*.log">
<Output TaskParameter="Include" ItemName="AfterClean_FilesToDelete"/>
</CreateItem>
<Delete Files="@(AfterClean_FilesToDelete)" />
<CreateItem Include="$(ProjectDir)\obj\" >
<Output TaskParameter="Include" ItemName="AfterClean_DirectoriesToDelete" />
</CreateItem>
<CreateItem Include ="$(ProjectDir)\bin\" Condition="'$(TargetExt)' != '.exe'" >
<Output TaskParameter="Include" ItemName="AfterClean_DirectoriesToDelete"/>
</CreateItem>
<RemoveDir ContinueOnError="true" Directories="@(AfterClean_DirectoriesToDelete)" />
</Target>
3) In my continuous integration MSBuild project I check and make sure that all proj files have #1:
<ItemGroup>
<!-- Exclude viewer acceptance tests as they must compile as x86 -->
<CheckProjects_CsProjects Include="**\*.csproj" />
</ItemGroup>
<Target Name="CheckProjects">
<!--
Look for C# projects that don't import CommonSettingsCs.targets
-->
<XmlRead XPath="//n:Project[count(n:Import[@Project[contains(string(), 'CommonSettingsCs.targets')]]) = 0]/n:PropertyGroup/n:AssemblyName/text() "
XmlFileName="%(CheckProjects_CsProjects.Identity)"
Namespace="http://schemas.microsoft.com/developer/msbuild/2003"
Prefix="n" >
<Output TaskParameter="Value" ItemName="CheckProjects_CsMissingImports"/>
</XmlRead>
<Error Text="Project missing CommonSettingsCs.targets: %(CheckProjects_CsMissingImports.Identity)"
Condition="'%(CheckProjects_CsMissingImports.Identity)' != ''" />
</Target>
This prevents developers from forgetting to add #1. You could create your own project template to ensure that al new projects have this by default.
The advantage to this approach is setting up a new source tree enlistment doesn't involve anything more than getting the current source tree. The downside is that you have to edit the project files once when you create them.