Just set intrascale on the basis of the connectivity #490
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This PR simplifies the calculation of the end-state intrascale matrices, basing it entirely on the end-state connectivity determined from the bonding. The complicated logic is no longer needed, which (originally) assumed that your were building the matrices from the end-state intrascale properties, which is no longer the case.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]