Cytopath

* Distance matrix between simulations uses PCA coordinates by default.
* Projection coordinates are different from trajectory coordinates.

Changelog:

- Replaced two-stage clustering with single-step HDBSCAN and added a minimum support parameter for clusters.
- Specifying number of clusters per end point is no longer supported and using the cluster_num parameter will raise an error.
- Plotting functions were updated for more informative visualisation.
- Default values were adjusted in accordance with other changes.