Ttclust

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).

Two new arguments added:
- `axis` to force "Frame" label in the barplot axis (use `-axis frame`)
- `limitmat` to decrease the trajectory size limit to generate the distance matrix. It is now `100000000` but if the distance matrix is too long to generate, you can just decrease this limit with `-limitmat 10000`