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The ArcGIS Runtime does not do anything to clean up the package unpack folder (C:\Users\<username>\Documents\ArcGIS\Packages) in order that the unpacked package contents can be reused between application sessions. The original package file and the unpacked contents will first be compared to determine whether the package is newer in which case it will be unpacked again.
Any files/folders in %temp% called %TEMP%\arcgisruntime_xxxx should be cleaned up during the local server shutdown. If this is not the case, and you have a reproducer application/data that you can share, we'd be keen to test it.
Providing API support for specifying the unpack location and the temp location is on the future roadmap.