Let's get rid of the "Code" directory

In accordance with #86 (closed) this proposal suggests that instead of having a repository layout as

ExaHyPE-Engine/
├── Code
│   ├── ApplicationExamples
│   ├── Applications
│   ├── CodeGenerator
│   ├── ExaHyPE
│   ├── ExternalLibraries
│   ├── Miscellaneous
│   ├── Peano
│   ├── Toolkit
│   └── UserCodes
├── LICENSE.txt
├── README.md
└── RUN.sh

we should have this simpler one:

ExaHyPE-Engine/
├── ApplicationExamples
├── CodeGenerator
├── ExaHyPE
├── ExternalLibraries
├── LICENSE.txt
├── Miscellaneous
├── Peano
├── README.md
├── RUN.sh
├── Toolkit
└── UserCodes

The idea is when having not a Code repository, people don't even plan to create something non-Code-ish in the repository. Which is a good idea.