[lohedges]

This PR adds a flat-bottomed distance restraint, FlatBottomBondRestraint(s), so that truncated-protein FEP setups can move from SOMD1 to SOMD2. The potential matches SOMD1's distance restraint, E = k * (|r - r0| - rfb)^2 when |r - r0| > rfb and zero otherwise, using the same units. SOMD1 (reql, kl, Dl) values therefore map directly onto r0, k and rfb. The restraint is created with sire.restraints.flat_bottom_distance() or sire.restraints.flat_bottom_bond(), and is converted to OpenMM as a CustomBondForce that is scaled by the lambda lever like the other restraints.

The PR also fixes some existing restraint bugs found during review:

• operator+ on seven restraint containers returned the unmodified left-hand operand, so a + b silently dropped b.
• Converting restraints to OpenMM read past the end of the atom map when a restraint index was outside the system. It now raises an exception.
• The bond, inverse bond and Morse centroid constructors named the wrong atom in the overlap error, and called squeeze() inside the loop.

The restraints tutorial has a new section for the flat-bottomed restraint, and the changelog has an entry for each change. Some files have also been reformatted by the pre-commit hooks.

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have added a test for any new functionality in this pull request: [y]
• I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [y]
• I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
• I confirm that I have permission to release this code under the MIT license (the Python API) or the LGPLv3+ license (everything else), as described in the LICENSE file: [y]