Fix case sensitivity issue when building on Linux

Building with MonoDevelop 5.4 and Mono 3.10.0 on Linux gives this error:

    /opt/mono/lib/mono/4.5/Microsoft.Common.targets: Error: Cannot copy /mnt/data/dev/games/MonoGame/Tools/Pipeline/app.config to /mnt/data/dev/games/MonoGame/Tools/Pipeline/bin/Linux/AnyCPU/Release/Pipeline.exe.config, as the source file doesn't exist. (Pipeline.Linux)