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[SofaBaseTopology] Fix right setDirty/clean topologyData #889
Cherry pick last useful changes from PR #788
All topologyData were set to dirty as soon as a topology modification was done. Check the Data link and set/clean dirty only topologyData link to the topology array modified.
NB: factorisation will be done as soon as everything work fine. Having several methods per topology make my eyes cry but it helps to follow the data link for debug.
Reviewers will merge only if all these checks are true.