fix: pixi init for pyproject.toml

[Hofer-Julian]

By creating the directory structure hatchling requires

Fixes #1903
Fixes #1941

[Yura52]

If I understand correctly, after this PR, pixi will unconditionally generate the src-based layout regardless of the Python project type (library or application). The recently released uv==0.4 became more adaptive w.r.t. the src/ folder depending on the project time. Perhaps, this can be relevant for pixi as well.

[Hofer-Julian]

Thanks for the hint @Yura52.
That is indeed something to investigate in the future.