Bugfixes, bond support, and others

This release incorporate a few new features. The main ones relates to connectivity support. Bonds can now be added based on a distance criterion, and the bond-tree can be used, for instance, to detect rings.

Several bugfixes are also incorporated.

There is a minor API break in this release. The xtb handle used to automatically optimize structures before performing an MD simulation.
It does not do so now.