Payload contains two or more files with the same destination path 'System.Diagnostics.Tools.dll'

The problem has solve it self. An update to the latest version of Microsoft.NETCore.UniversalWindowsPlatform has solved it.

It look like that library A was compiled against version 5.1.0 and library B was compiled against version 5.2.2. Because my project was on version 5.1.0 there was a conflict situation. I does not understand why I have no conflict if I switch the UWP version.

If I use the library B with the old UWP version there was also no conflict.

Just in case it may be useful to others encountering the same error - "Payload contains two or more files with the same destination path..." - which can be caused by a variety of reasons related to the labyrinth of NuGet packages, one remedy for such NuGet related errors is clearing the cache, or simply deleting the problematic NuGet package folder: C:\Users\user\.nuget\packages\

This is based on my own experience of dealing with similar errors including this particular one.

Edit (2018-07-22): I have been having good luck in dealing with this and similar problems by simply restarting Visual Studio. Probably Microsoft is getting to this bug finally. I get this kind of problems only when building a release version.

In my case, I had "Any CPU" option selected so it was compiling the same library for both versions. Selecting x64 solved the problem for me.