Use Pitchfork project layout conventions

[doganulus]

We could adopt the Pitchfork project layout, which provides a well-structured and widely recognized directory organization.

According to these conventions, the top-level structure would look like:

|-- build/
|-- include/
|-- src/
|-- tests/
|-- examples/
|-- external/
|-- data/
|-- tools/
|-- docs/
|-- libs/
|-- extras/

To align with this layout, we should reorganize the repository by moving all source files under src/, and distribute the remaining files accordingly.

[doganulus]

See the branch and the pull request addressing this issue.

I will wait for some feedback before actually merging such an extensive change.