Allow ability for probe/frame/timepoint grouping to be interpreted as explicit permission rather than prohibition (dually implied implicit permission)

[vreuter]

With the solution for #71 , we now have regional_probe_groupings in the config file, as a list-of-lists. Each collection is interpreted as specifying a prohibition on probes being in close proximity, i.e. timepoints for which spots should be mutually excluded if spots' centroids are too close to one another. This is a narrowing of the default restriction that no spots may be in close proximity to one another. Viewed from the dual perspective, it's an implicit permission: spots detected in timepoints that aren't declared in the same grouping are permitted to violate the minimum distance (min_spot_dist threshold).

For new work by @TLSteinacker , we need to allow an explicit permission to be encoded. That is, timepoints grouped together are the ones which will be permitted to violate the minimum distance threshold of min_spot_dist. Spot pairs from timepoints not declared together, then, will be forbidden to occur close together.