Automatic Resolution of Inconsistencies During Merge
LemonTree automatically resolves all inconsistencies it is able to when writing a model.
As this mechanism is improved with each released version of LemonTree, one of the most important ways to resolve inconsistencies not cleaned up by the Enterprise Architect Integrity Check is to merge the model with the currently released of LemonTree (or the most current version you're allowed/able to use).
Unfortunately, there is currently no way to manually trigger this mechanism other than performing a merge. We plan on introducing this as a separate feature of the LemonTree Enterprise Architect Addin in the future, though.