Let's get rid of the "Applications" folder

This message goes mostly to @di25cox and @ga96nuv as they have worked in folders in https://gitlab.lrz.de/exahype/ExaHyPE-Engine/tree/master/Code/Applications in the last seven days:

As Vasco and me figured out in the last days at #67 (comment 38114),

• ApplicationExamples currently holds the public applications
• Applications currently holds the private applications

However, the only "private" applications so far (Z4) moved to an own repository. I would hence suggest to merge the folders Applications and ApplicationExamples.

Please let me know if you have any objectives against.