Fixed JSON files with non-contiguous segments.
Fixed JSON files with non-contiguous segments.

The resulting trees are not equivalent to the initial ones. All
offending branches were split and their non-contiguous part was moved
directly below the root.

eth-cscs/nestmc-proto,halfflat/arbor,halfflat/arbor,halfflat/arbor,halfflat/arbor,halfflat/nestmc-proto,halfflat/nestmc-proto,halfflat/arbor,eth-cscs/nestmc-proto,halfflat/nestmc-proto,eth-cscs/nestmc-proto