Ttclust

Include small bugs fix and code to remove/check warnings.

The new version of matplotlib causes a bug with the dendrogram graph. It is now fixed

This version correct a bug introduced in 4.8.4 that caused an issue in the RMSD distance matrix.

- Numpy matrix file names are now hashed with MD5 if the name is too long
- The alignment is now included in the linkage matrix filename.

Bug fixed with distance matrix calculation

MDTraj's RMSD function realigns the protein which is incompatible with the `-sa` argument.

The RMSD is now calculated by a homemade implementation to combine with Numba for faster calculation (but still a little slower than MDTraj).