System.getProperties should return the last value set by setProperties

[mlopatkin]

Current implementation of the JVM doesn't do defensive copying when setting system properties wholesale. The provided Properties instance is stored. The instrumented Gradle functions do not follow this, which can lead to subtle behavior differences.

Note, that there is no need to have a finer-grained tracking of the property reads after setting the properties for the configuration cache purposes, because it is not possible to affect them externally anyway. We still need to capture them tat the end of the configuration phase o be able to restore them when reusing the cache.