Fix inconsistencies in merge code #488
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This PR introduces some inconsistencies in the merge code introduced by the ROI merge feature.
The wrong connectivity object was being used as a reference when comparing end state connectivities to determine whether rings have been broken or have undergone a size change.
In certain cases, comments within the code referred to the old merge implementation, so were inconsistent with the actual logic of the code.
Several loops used in the reconstruction of the intrascale matrix were incorrectly indented.
I confirm that I have merged the latest version of
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]I confirm that I have permission to release this code under the GPL3 license: [y]