Restructure Parcels to use `src` layout

xref #1965 

---

> We can avoid this completely by using a `src` layout. If we're restructuring soon anyway, might as well do that. 

 _Originally posted by @VeckoTheGecko in [#2214](https://github.com/OceanParcels/Parcels/issues/2214#issuecomment-3292613866)_