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When using CallTarget, any Items or Properties created within the called target should be destroyed when the flow control returns to the caller. This is not the case with xbuild, but is with msbuild.
In this simple example xbuild will generate the output "1;2;3;4;5;1;2;3;4;5" and msbuild will generate "1;2;3;4;5" as expected. I've attached the build script, and logs for xbuild (126.96.36.199) and msbuild (4.0):
<Message Text="Items in Collection before CallTarget: @(Collection) "/>
<Output TaskParameter="TargetOutputs" ItemName="Collection" />
<Message Text="Items in Collection after CallTarget: @(Collection) "/>
<Collection Include="1;2;3;4;5" />
If you remove the 'Outputs' then xbuild outputs "1;2;3;4;5" and msbuild outputs nothing.
Created attachment 5558 [details]
sample script of the problem, logs from xbuild and msbuild.