Remove all remaining references of Guava's Files class.

[LukasMansour]

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Motivation: Closes #3808

Modification: Removes the last instances of com.google.common.io.Files and replaces most of them with the JDK alternative. (Also required updating one or two guava classes, like the TreeTraverser)

Result: The remaining references of Guava's Files class are removed and some small tweaks to reduce the usage of Guava were done.

Signed-off-by: Lukas Mansour [email protected]