Improve "src" folder structure (namespace)

Engine and Engine API is applying the "newish traditional" source folder pattern, where all the source code is located in src. See this comment for reference.

Current implementation

All source code is already located in src.

Expected implementation

Source code should be nested in some additional package named after the project-name. For example src/engine and src/engineapi. As per PEP-8 underscores should be avoided, if possible.

The namespace for import statements in contrast should only require the engine prefix, like engine.foo.bar. Not having src part of the namespace.